I was especially curious as the novel and it's writer Liu Cixin are incredibly popular in China but the scenes describing things like Struggle Sessions, and the radicalism of the Red Guards seem like scathing descriptions that one would assume would be censored by the CCP, yet Liu has even spoken in support of the Chinese government and the novel has been adapted into a TV series in China. Are the negative consequences of the Cultural Revolution largely recognized in China?
For the short and official answer: yes it is recognized as a bad thing.
For the longer answer... it's complicated.
In a certain way the recognition of the Cultural Revolution (CR) is a very simple affair. The CCP leadership that eventually came into power after Mao's death (1976) were, well, almost all victims of the CR themselves. Deng Xiaoping, the succeeding paramount leader of China, was purged not once but twice during the CR. As a prominent reformist in the Poliburo, he was subjected to a whole "Criticize Deng" (批邓) campaign by the Maoists to publicly disgrace him. Among many other things, he was exiled to work in a tractor factory for four years, and his son was killed under chaotic circumstances by the Red Guards. So it is not hard to imagine how Deng and his reform-minded supporters felt about the CR when they came into power in 1978.
Almost immidiately the CCP under Deng launched the Boluan Fanzheng ("correction and normalization") movement to de-Maoize China: reverting extremist policies and rehabilitating millions of victims. These comprehensive socioeconomic reforms would later pave the road to the famous Gaige Kaifang ("reform and opening-up") and see China transition from a Maoist pariah state into the state capitalist powerhouse today. If you want to know more about Deng Xiaoping and how he changed China after Mao, I seriously recommend Ezra Vogel's Deng Xiaoping and the Transformation of China.
When it comes to the official evaluation of the CR, in 1981 the CCP Eleventh Central Committee passed the Resolution on Certain Questions in the History of Our Party Since the Founding of the People’s Republic of China. This is a very big deal. Throughout the CCP's 100-year history only three such "history resolution" documents have been passed (the first in 1945, this second one in 1981, and the newest one this year in 2021) and they represent the CCP's official position on its own history. In the 1981 resolution, the opening lines for the chapter on CR straight-out says:
The “Cultural Revolution", which lasted from May 1966 to October 1976, was responsible for the most severe setback and the heaviest losses suffered by the Party, the state and the people since the founding of the People’s Republic."
You can go read the full document if you're interested; to date this still remains the offical narrative of the CR in China. One of the "benefits" for an authoritarian party-state is that once the official position has been decided, the entirety of the state apparatus will then follow suit without objection. So yes, it is perfectly normal for Liu Cixin to begin his Three-Body Problem from the horrors of the Cultural Revolution, and for the novel to subsequently achieve global success and become the pride of modern Chinese sci-fi.
However,
How the issue is actually treated by the Chinese people in Chinese society today, is much more nuanced. Unfortunately for this part I can only speak from personal experience. Of course, nobody would jump out and say the CR was good (even though there's been an alarming resurgence of Maoism in China lately). Despite the CCP's official condemnation of the CR, it is still very much a sensitive topic given China's suppressive environment of censorship and self-censorship. Most people would not openly talk about it in public, and when they do it's often in passing and through careful euphemisms. Textbooks still prefer to use the term "decade of turbulance" (十年动乱) instead saying the words "Cultural Revolution" (文革) out loud. Despite a wealth of scar literature (伤痕文学) in the from of novels and memoirs that shares individual experiences from the CR, there is still very little systematic study of the subject by professional historians in mainland China (most research come from Hong Kong). The events of the Cultural Revolution, much like the Great Leap Forward and other disastrous Maoist campaigns, exist in a weird limbo where they are both officially acknowledged and yet still taboo.
Unlike with some other events (i.e. the Tiananmen Incident), there is no rule saying you can't talk about the CR — but the reality is that most people still don't, much less publish books about it, much much less publish books that become popular. Liu Cixin could do it because he was already an established author before Three-Body Problem, and he smartly did it through a beloved fictional medium, and because his novel is actually super good. Another great Chinese novel that puts emphasis on the history of the CR is Drawing Sword (亮剑) by Du Liang from the 2000s — a much more liberal time in China when it came to expression, mind you — a historical fiction about a legendary miltiary officer's rise and fall in 20th-century China. The first half of the book focuses on his rise through the ranks during WWII and the subsequent Chinese Civil War, becoming a general of the PLA in the new People's Republic; the second half is about his tribulations, disgrace, fall, and ultimately death during the Great Leap Forward and Cultural Revolution. The novel was immensely popular in China (on a similiar level as TBP today) and adapted into an even more popular TV series. But the series, for whatever reasons, conveniently chose to end after the first arc.