Nee studied biology at the University of California at Los Angeles, and history at the University of California at Santa Cruz where he graduated in 1967. He was accepted for graduate studies that year at Harvard University and was a co-founder of the Committee of Concerned Asian Scholars—a group of faculty and graduate students who opposed America’s intervention in Vietnam.
As a graduate student he wrote with his wife Brett de Bary, Longtime Californ’: A Documentary Study of an American Chinatown published by Pantheon Books. He took a leave of absence from graduate school in 1972 to work as a freelance writer in San Francisco and Tokyo. Nee traveled to China in 1974 to study Chinese at Beijing University.
In 1975 he returned to Harvard University to complete his dissertation in Sociology, which he received in 1977.
Nee was an assistant and associate professor of sociology at the University of California at Santa Barbara from 1977 to 1985. He joined the tenured faculty of the Department of Sociology at Cornell University in 1985 and held the Goldwin Smith Professor of Sociology from 1991 to 2011.