The major components of NIBS are its research laboratories and core facilities. The Principal Investigators (PIs) are selected from a highly competitive international applicant pool by a Selection Committee that evaluates the applicants and recommends candidates for appointment. A PI shall serve for 5 years and the reappointment is contingent upon academic evaluations by his/her peers in the closely related research field. Heads of the core facility will be appointed by the Director.

NIBS is governed by its The Board of Trustees (BOT), which is responsible for institute policy and consists of representatives from eight agencies, including the Ministry of Science and Technology (MOST), National Development and Reform Commission (NDRC), the Ministry of Education (MOE), the Ministry of Health (MOH), the Chinese Academy of Sciences (CAS), the National Natural Science Foundation of China (NNSFC), and the Beijing Municipal Government. MOST and the Beijing Municipal Government are primarily responsible for overseeing the operation of NIBS and provide the major sources of funding.

The Director is responsible for the daily operations of NIBS under the leadership of the BOT. The BOT shall further select well-known scientists to serve on a Scientific Advisory Board (SAB). The SAB is consulted on issues related to PI appointment and research development. Its mission is also to select and advise the Director and provide support as needed to the BOT. The initial term of appointment to the SAB is three years, and its members may be reappointed.

In April 2003, the BOT accepted the recommendation of the SAB and appointed Dr. Xiaodong Wang, a member of the U.S. National Academy of Sciences and a biochemist and cell biologist from the University of Texas Southwestern Medical Center, and Dr. Xingwang Deng, a plant biologist from Yale University, as Co-Directors of NIBS. Dr. Xiaodong Wang accepted the second-term appointment as the NIBS director and moved back to Beijing full time in 2010.