During the 1950s, under Senator Joseph McCarthy, there was a witchhunt for leftist economists, and Thorner would not divulge the names of his leftist friends. Thus he lost his job and a government-funded fellowship for a project in India. He borrowed money from his parents and left for Bombay in 1952 along with his wife He travelled extensively in Indian villages and continued to work on agricultural economics.
Academic work
His stay in India resulted in three books on Indian agriculture. The first one, The Agrarian Prospect in India published in 1956, was based on his direct observations and interactions with villagers in several parts of India. His two subsequent books were published after he left India and were Agricultural cooperatives in India, a collection of papers on agriculture and economic history and Land and Labour in India. Both were analytical works, examining the impact of policy on Indian farmers and boldly questioned existing statistics, reports and data, where they were poor or unreliable. In Bombay, he built a large circle of friends and admirers and contributed to the Economic and Political Weekly. He also lectured at the Delhi School of Economics. His interactions with PC Mahalanobis resulted in his contributions to the Planning Commission to refine the tabulations of the 1961 census. The previous tabulations for the 1881 and 1911 Indian census developed by Colin Clark showed a significant decline in the share of Indian workforce in various industrial sectors implying drastic deindustrialization. Thorner reexamined the census data and convincingly argued that the tabulations used by Clark were misleading. He concluded from the data that de-industrialization in India was very modest in the twentieth century, and any de-industrialization had occurred in the late nineteenth century, contrary to prevailing belief.
Later life
Due to desire to return to a university and partially due to economic reasons, he left India in 1962 after spending ten years, to take up an academic position at School for Advanced Studies in the Social Sciences. He edited the works of Harold H. Mann, an economist and Alexander Chayanov. He was instrumental in introducing Chayanov's work to the English-speaking scholars. He continued to visit South Asia often and helped with the escape from persecution of some intellectuals from Dhaka during the Bangladesh Liberation War After a brief period of illness, he died in 1974.