The Center has five governing institutions: the Steering Committee, the Management Committee, the Academic Committee, the Development Cooperation Committee, and the Secretariat. Among them, the Steering Committee is led by the Ministry of Science and Technology of the People's Republic of China and consists of ministries and commissions such as the Ministry of Science and Technology of the People's Republic of China, the National Health Commission of the People's Republic of China, the Ministry of Education of the People's Republic of China, the Ministry of Foreign Affairs of the People's Republic of China, the China International Development Cooperation Agency, and the National Agency for Disease Control and Prevention. The 13-member Management Committee consists of a Center Director, an Executive Director (currently the Dean of the School of Public Health), three Deputy Directors, and eight members to manage the work of each research sub-center. The Academic Committee has 24 members, including 10 domestic experts and 14 experts from ASEAN countries, plays a technical guidance role for joint scientific discussions, technical exchanges, and strategic development. The Secretariat Office is composed of 6 persons， and is located in the Department of Global Health, School of Public Health.

Based on the operation mechanism of "one center, multiple research networks", the Center has set up sub-research centers to form different research networks, which will be gradually expanded according to the Center's construction and development needs. Currently, ten sub-research centers have been established, and relevant research teams and individuals from China and ASEAN partners can join the corresponding sub-research centers according to their research areas to form a research network in their respective research areas and carry out research and cooperation under the coordination of the sub-research centers. The ten corresponding sub-research centers include China-ASEAN Health Governance and Development Cooperation Research Center, China-ASEAN Communicable Disease Prevention and Control Strategy Research Center, China-ASEAN Health Big Data Research Center, China-ASEAN Health System Construction and National Health Coverage Research Center, China-ASEAN Maternal and Child Health Research Center, China-ASEAN Health Technology and Product Innovation and Transformation Research Center, China-ASEAN Medical Product Regulatory Cooperation Research Center, China-ASEAN International Cooperation Research Center for Health Emergency Response, China-ASEAN Research Center for Climate Change and Environmental Governance, and China-ASEAN Research Center for Whole Life Cycle Health Promotion.