The "Mongolian origin" really had relatively little to do with it. By the upwelling of the Red Turbans as of the 1340s, the larger whole of China had basically come to largely accept and work within the Yuan orthodoxy, with very few hold-outs left.
But, well, things really started to - to put it gently - suck rather a lot round about 1340 and going forward. This isn't to say that things ere just "hunky-dory" before that. No, the Yuan regime had been facing down a spiraling currency crisis virtually since its inception. In itself, this was not great... but not terrible. Even without further conquests (which by 1340 just had simply not been "a thing" for ~50-60 years at this point) could be dealt with through raising taxes further on the populace at large... or even ~*GASP*~ potentially cutting down on the annual gifts dispersed among the Mongol princes to keep them fat & happy. Again... it wasn't a great system, but on the other hand, there had actually be far worse that survived far longer.
Instead, we get a real sea-change that upsets the status-quo... not just for Yuan China, but the world overall: relatively quick climate change and (of course related) an outbreak of one of the worst pestilential outbreaks of disease humanity has ever faced...
Between the mid-10th and the mid-13th century, the Earth’s climate had gone through an epoch very boringly called the Medieval Warm Period, in which large parts of the planet were the warmest and wettest they’d been since the 3rd-4th centuries, and the warmest they’d be right up until the mid-20th century blew right by them both. Now it is important that I throw in so qualifiers here about what I mean when I talk about global shifts in climate conditions.
Number 1: they’re not uniform. Some places were still cold during the warm period, and some places even colder than usual! Some places were warmer than usual turning the cooling period that I’ll talk about in a minute. That’s the thing with a vast, hypercomplex system like the Earth’s climate – it’s vast, and hypercomplex, and defies a simple, uniform answer. What we’re looking at here, however, is an overall upward shift in global mean temperate, as a whole, for a period of several centuries. Number 2: warmer/cooler dynamic is often accompanied by, or even more directly observed as, wetter and/or drier climates. Warming conditions tend to increase moisture in the atmosphere, and thus make conditions wetter – and the opposite is true for cooler conditions, leading to increase patterns of drying. If you want it is really easy-to-picture terms: think of an electric air conditioner and how it will tend to dehumidify the room it’s in.
Alright, so by the 14th century, the world has moved out of the Medieval Warm Period and is well on its way toward plunging into an even longer cold period most commonly known as the Little Ice Age that would last, more or less, until about the mid-19th century (though it’s a bit of a misnomer, as it was not actually an ice age). Now, this might have been caused by lower solar activity, or a change in the axial tilt of the Earth so that the northern hemisphere was experiencing shorter summers (and I guess I should put in a third qualifier in here, that virtually all of the data we have of both of these periods comes from the northern hemisphere, since that where both the majority of people, and the majority of written records of such events were). It could also have had to do with a possible period of increased volcanic activity across the globe setting off something of a mild-ish volcanic winter for a few hundred years. It could even have to do with changes in the oceanic currents and how they cycled heat around the Earth (though again, it’s a hypercomplex system, and the atmosphere and ocean currents both affect each other greatly, so it’s probably a bit of a chicken-and-egg situation).
Regardless of the hows and whys, this planet-scale cooling and drying does much to explain the difficulties and disasters that were cropping up all across the Earth in the 14th century. Cooler, shorter, dryer summers meant lower crop yields, droughts, and increased levels of famines. This general decline in access to sufficient nutrition, over enough time, would generally weaken a human population, and especially their immune systems. It would also tend to get people a lot more “hangry” and willing to, say, stop working their failing farms and start more wars to get better access to things like food and supplies, leading to yet further suffering, starvation, and overall weakness. It’s can – and did – become a potent and lethal positive feedback loop of negative outcomes leading to even more negative outcomes, which in turn reinforce and exacerbate the first negative outcomes, and so on. And that leads us to our main character in the story of the Black Death – the microscopic rider on the pale horse: Yersinia pestis, the little plague bacterium that could.
Y. pestis’ native home is in the gut of fleas that themselves primarily live and feed on any number of little rodents and varmints all across Eurasia and North America. As that is its native lifecycle, being transmitted back and forth between rodents and fleas, it doesn’t tend to negatively affect either of those species, or at least kills the rodents at a slow enough pace to ensure further transmissibility for the bacteria. Where things get bad is when y. pestis finds itself in a familiar-but-not-that-familiar different species of mammal, such as a human being, which it is not designed to live in. In the absence of any of the usual defenders checking and slowing its grow cycles, y. pestis goes hog-wild within the unprepared body and tends to destroy it utterly and rapidly – AKA the Black Death!
For the longest time, it was simply understood as a matter of course that the Black Death was transmitted from East Asia, across the Silk Road, westward to the Middle East and Europe via caravansaries and merchant vessels – and so ipso facto, it was a new disease carried over from east to west thanks to increased human interconnectivity; thanks a lot, globalization! Thanks a lot, Mongols! But as of 2013, new evidence pretty much blew that explanation out of the water. DNA testing of bones of the victims of the Justinian Plague that devastated the Byzantine Empire and wider Europe in the mid-6th century, conclusively determined that those plague victims had been killed by pretty much the exact same strain of yersinia pestis as would grip Eurasia in the 14th century! So it wasn’t the Mongols bringing it over to Europe… because it had already been lurking in and around Europe for more than 800 years! So that means we get to blame the Xiongnu and the Huns instead! Yaay!
So, why did the plague go relatively quiet up until right then, and then absolutely explode? If your answer was “it sounds like he’s going to say climate change,” you get a gold star! A drying, cooling trend in the climate that shrank growing seasons didn’t just affect human-grown crops, but their wild counterparts across the Eurasian grasslands, as well. It’s likely that many of those rodents – and the miniature, biting harbingers of doom riding them, would have flocked to areas where the was more food – which of course tended to be areas with much higher concentrations of people, like medieval farms, cities, and army camps. Yet when we look at the Black Death, even if we go by the old (and now disproved) hypothesis that it “came from China via the Silk Road,” its impossible not to notice that the Islamic world and Christian Europe take up almost the entire space of “The Story of the Black Death.” We rarely ever hear of it causing the sort of absolute devastation in East Asia as we do across Europe, to the tune of 30-60% of entire populations dropping dead. It’s well worth asking: what is up with that?
Well, the climate-theory of its rapid spread in the 14th century might help to explain that, at least – maybe the conditions in western Asia and Europe were different enough from East Asia that rodents were somewhat more likely to migrate to cities. That doesn’t seem very convincing, though. What seems to be the far more likely explanation is not that Yuan China was less affect by y. pestis than other regions of Eurasia… but rather that, though it served as The Primary Apocalyptic Event of the western world at that time… the outbreak of plague in China was but a single aspect of a far larger and even more devastating calamity.
Throughout the 1340’s and 50’s, the History of Yuan records not “a plague” but overlapping series of several plagues ripping through the empire, on top of recurring periods of drought, flood, and famine. And then, of course, there were the widespread peasant uprisings, millennialist apocalypse cults, and good old-fashioned full-scale rebellion and dynastic overthrow… all in the course of a scant few decades. The Yuan had never been very good record-keepers – the absolute travesty that is their entire census logs stand as testament to their shoddy workmanship on that account – and the we should all be thoroughly not shocked that their regime rapidly declining and being forcefully ejected from the Yellow River Valley didn’t help that effort at all. All of that to say: it’s hard to know exactly how bad the damage was altogether, much less from any specific source, because the general chaos of the era virtually ensured that no one was stopping long enough to take very good notes.
While we’re on the topic of population and the data we have about this period, I’d be absolutely remiss if I didn’t bring up one of the most frustrating aspects of the Yuan period: its census taking and population records. They have been since they were first recorded maddening historians trying to piece together what went on, and to what extent it affected the populations of northern and southern China.