After graduating, he joined the CCP, started working at the Institute of Modern Physics and became involved in China's secret atomic bomb program,[8][9] while Li stayed at Peking University as a junior faculty member.

Fang was not immediately expelled from the party, because he played a lesser role in writing the letter, and also because he had left Peking University, where the punishment was particularly severe.

In August 1958, Fang was reassigned to the faculty of the University of Science and Technology of China (USTC), which was located in Beijing at the time.

[12] In spite of his experience in the anti-Rightist campaign, Fang published an article in the Guangming Daily, encouraging the independent thinking of students.

Later, on the recommendation of Qian Linzhao, he became an associated member of a research group led by Li Yinyuan at the Institute of Physics, Chinese Academy of Sciences.

That year, as part of the effort of cleansing Beijing of "undesirable elements", Fang was to be removed from the faculty of USTC and sent to work in an electronics factory in Liaoning province.

In 1969, along with other universities and research institutes, USTC was ordered to be evacuated out of Beijing, ostensibly in anticipation of an impending invasion by the Soviet Union.

Upon arriving in Hefei in 1969, Fang, along with other "problematic members" of the faculty, were sent to do hard labour for "re-education by the worker class" in a coal mine.

Professor Dai Wensai, the most well-known Chinese astronomer at the time and chair of the Astronomy Department of Nanjing University, also supported Fang.

In the late 1970s, he and his group used the luminosity of selected radio quasars to measure the Hubble diagram, and with data available at the time, suggested that the universe may be closed (Fang et al., Acta Astronomica Sinica 17, 134 (1977)).

Fang also carried out research on topics including neutron stars, black holes, inflation and quantum cosmology.

[18] He invited Stephen Hawking to visit China in 1985,[19] and organized the International Astronomical Union conference IAU-124 on "Observational Cosmology" in Beijing in 1986.

[citation needed] Fang was also the first scientist in China to write popular accounts of contemporary astrophysical developments, such as cosmology and black holes.

Fang's book, "Creation of the Universe" (Yuzhou de chuangsheng in Chinese) which was published in 1987, introduced basic cosmological ideas, and influenced a large number of physics and astronomy students growing up in the 1980s in China.

Fang also begin to write essays for publication in popular magazines, and give lectures on a variety of topics in universities, though usually not in USTC.

In late 1986, Fang, together with Xu Liangying and Liu Binyan, wrote letters to a number of well-known "Rightists" from the 1957 Anti-Rightist campaign, suggesting a meeting in memory of that event.

[24] In December 1986, college students demonstrated in over a dozen Chinese cities in demanding greater economic and political freedoms.

Because of his refusal, Hu Yaobang was dismissed from his position as General Secretary in January 1987, effectively ending his period of influence within the Chinese government.

[citation needed] In February 1989, Fang mobilized a number of well known intellectuals to write an open letter to Deng Xiaoping, requesting amnesty for the human right activist Wei Jingsheng who was then in prison.

Fang and his wife had exchanged ideas about Chinese politics with some students of Peking University, including Wang Dan and Liu Gang.

[26]: 148 On June 5, 1989, the day after the government cracked down on the Tiananmen Square protests, Fang and Li sought asylum at the U.S. embassy in Beijing, accompanied by U.S. academic Perry Link.

[26]: 148  Fang and Li were initially turned away, but Jeffrey A. Bader, then acting director of the Office of Chinese and Mongolian Affairs at the State Department, used very strong language to order the embassy to reverse their decision.

His later research includes the study of non-Gaussianity in the cosmic microwave background anisotropy, Lyman alpha forest, application of wavelets in cosmology, turbulence in intergalactic medium, and the 21cm radiation during the Reionization.