Lin taught at Peking University since 1986, he became a professor at the College of Chemistry and Molecular Engineering, Peking University (CCME) in August 1995. In July 1997 he became the Deputy Dean of the College of the CCME, rising to President in April 2001. He became the Vice-President of Peking University in September 2002, Executive Vice-President of Peking University in December 2004.
He was honored as a Distinguished Young Scholar by the National Science Fund for Distinguished Young Scholars in 1997.
In December 2010 he was promoted to become the President of Chongqing University, a position he held until June 2013. Then he was appointed the President of Zhejiang University, he remained in that position until February 2015, when he was transferred to Beijing and appointed the President of Peking University.