In August 1949, he assumed the post of president of Zhejiang University. At the same time, he was a member of the Central People's Government, vice director of Central Finance and Economy Committee and vice director of East China Military and Political Committee. In 1951, he became president of Peking University. In the early 1950s, he started research into China's rapid population growth. In his famous article "New Population Theory", he expounded on the problem in a systematic way, arguing the population was growing too rapidly. He believed that between 1953 and 1957, the annual growth rate of Chinese population might have exceeded 20‰, a figure drawn from the 1953 national census. He calculated that if the number of the Chinese grew by 20 births per 1,000 a year continuously and unchecked, in 30 years the actual population would far surpass the previously predicted figure. He also analyzed the necessity and urgency of population control in regard to accelerating capital accumulation, promoting science and technology, raising labor productivity, improving people's material and cultural standards and increasing industrial materials; there should be no delay in population control, otherwise problems would become thornier and more difficult to solve in the future. If the government took no action in restricting population growth, the peasants might become disappointed and dissatisfied. He put forward the idea of a regular national census and suggested including population control into China's Second and Third Five-Year Plan.
However, on January 4, 1960, he had to resign from the post of Peking University president because of his "New Population Theory". It was not until September 1979 when his case was redressed that he again took the position of honored president of Peking University and reelected member of the Standing Committee of the 5th National People's Congress. On February 27, 1981, he was elected honored president of China Population Association. On March 29, 1981, he was elected advisor of the first council of China Economics League. He died of disease on May 10, 1982.
His major works include New Currency Theory, A Collection of Papers on Wartime Economy, My Economic Theory, Philosophical Thought and Political Stand, China's Foreign Exchange, On China's Bank, China's Tariff Problems, A History of Capitalism Development, China's Economic Reform, Introduction to Economics, New Population Theory (Republication) and A Collection of Economics Papers by Ma Yinchu (I, II). In August 1993, he won the "special honor award" in the first China Population Award.