Being the Mongol Empire one of the biggest in history, why is it that nowadays Mongolia only has 3 million habitants? What happened to their civilization and the decrease in population ? They are a large country (size) and the majority of the east asian countries are dense in population...
Mongolia doesn't exactly have the best habitation standards. In the south, you have the inhospitable Gobi Desert, in the west the beautiful yet secluded Altai mountains, and almost everywhere else is forest, taiga or steppe.
Also, you ask "What happened to their civilization and the decrease in population?" The Mongols never had the largest population to begin with. At the time of Chinggis Khan, there was only ~2,000,000 Mongols. So, they have actually grown in the time from 1206-now.
And their civilization is very much still there, in one of the official definitions ("the society, culture, and way of life of a particular area"). Mongol life has barely changed since the time of the Yuan, other than the advent of the city. There is still a large nomadic population.
It's just their huge empire collasped under its own weight. So the civilization is still there, just not the empire.