* 2017: Qiu Shi Outstanding Scientist Award, Qiu Shi Science & Technologies Foundation
* 2017: Foreign member of the Chinese Academy of Sciences (As of 2023, member of the CAS after Chinese citizenship reclaimed)
* 2016: Member of the National Academy of Medicine 
* 2015: Albany Medical Center Prize
* 2015: Peter Debye Award in Physical Chemistry, American Chemical Society
* 2014: Fellow of the Optical Society of America
* 2013: NIH Director's Pioneer Award
* 2013: Ellis R. Lippincott Award, Optical Society of America and Society for Applied Spectroscopy
* 2012: Edward Mack, Jr. Lecture, OSU
* 2012: [http://www.chem.rochester.edu/howe/current.php Harrison Howe Award, Rochester Section of the American Chemical Society]
* 2012: Fellow of the American Academy of Microbiology
* 2012: Biophysical Society Founders Award
* 2011: Member of the National Academy of Sciences
* 2009: Ernest Orlando Lawrence Award
* 2008: Fellow of the American Physical Society
* 2008: Berthold Leibinger Zukunftspreis for Applied Laser Technology
* 2008: Fellow of the American Academy of Arts and Sciences
* 2007: Willis E. Lamb Award for Laser Sciences and Quantum Optics
* 2006: Fellow of Biophysical Society
* 2006: Fellow of the American Association for the Advancement of Science
* 2004: NIH Director's Pioneer Award
* 2003: Raymond and Beverly Sackler Prize in the Physical Sciences
* 1996: Coblentz Award