It's the latest example of the narrowing space for independent thought in modern China, and the ever tighter ideological controls being imposed under Xi's rule, foreign and domestic experts said. It is also at odds with China's ambitions to be a global power in academia, and undermines the chances of constructive debate over government policy.
"This strikes me as a Great Leap Backwards for Chinese academia," said Edward Vickers, an expert in Chinese education at Japan's Kyushu University.
In a speech in December, Xi declared that universities should be strongholds of the party, while teachers should be disseminators of "advanced ideology" and "staunch supporters" of Communist Party rule.
Six months later, the party's anti-corruption watchdog concluded an inspection of the nation's elite universities and accused 14 of them of ideological weakness for not making enough effort to teach and defend Communist Party rule.
It appears the higher education sector has learned its lesson.
The first to announce a research center dedicated to Xi Jinping Thought was Renmin University of China in Beijing, one of the nation's most respected higher education institutions with links to more than 200 other universities around the globe.
It opened the center on Oct. 25, just one day after thousands of party delegates unanimously voted to absorb the phrase into their constitution, alongside Mao Zedong Thought and Deng Xiaoping Theory.
"From the aspect of the development of our country, the establishment of the research center is of great historical significance," Liu Wei, president of the university and director of the new center, told Chinese media. "It is an important responsibility given to the school by our times."
While the party's ideology does merit serious study, say critics, the point of these centers is mainly to give the party some academic gloss and enhance its legitimacy.
The nation's top academics may not take them very seriously: Peking University already has a center dedicated to Deng Xiaoping Theory, and it is arguably peripheral to the main academic work of the university.
Nevertheless, the establishment of so many centers in such a short space of time symbolizes a significant shift in the political climate in which academics and students operate.
"While Xi is genuinely popular with many Chinese, attempts to reimpose this sort of crude ideological control in universities are not likely to lead to harmonious relations between academia and the party leadership," Vickers said.
"Many professors — especially in social science and humanities disciplines — find this more stringent ideological atmosphere highly demoralizing, though it is unlikely to provoke outright resistance."
The centers will also suck money away from other research projects, warned Wu Qiang, a former politics lecturer from Beijing's elite Tsinghua University.
"Universities, in the past five years, have transformed into machines and bases for directly serving the needs of ideology and the leadership," he added.
One man who has experienced the growing controls directly is Qiao Mu, a former journalism professor who was demoted at Beijing Foreign Studies Universities for his outspoken views, before resigning and finally leaving China in September to live in the United States.
He sees the centers as "shortsighted" and "a sign of degeneration" of Chinese universities as a whole.
"The universities, on one hand, want to use these centers to get funding and grants. On the other hand, they want to show their political loyalty," he said. "This goes completely against the principles of higher education, which is to promote the spirit of independence and the freedom of thought."
The move to put Xi's name in the constitution raised him to the level of Mao and Deng in the Communist Party pantheon. His "thought" will now become part of the syllabus in compulsory ideology classes taught to Chinese children and students, from primary school up to the university level.
Any challenge to his views will inevitably be seen as an attack on the party as a whole, and therefore as an attempt to undermine national security. Many experts see that as a dangerous path to follow.
Mao's attempt to jump-start industrial growth, known as the Great Leap Forward, disintegrated into a famine that killed tens of millions of people in the early 1960s. The party says it has learned the lessons of that period. But critics say the latest developments are symptoms of a party more inclined to lecture than listen.
"There is little doubt that the space for critical debate over public policy is being increasingly squeezed," Vickers said. "The party is evidently not in listening mode — but is intent on message control, at every level."
Luna Lin contributed to this report.