The affiliated units of HMU include: College of Basic Medical Sciences, College of Public Health, College of Pharmacy, the 1st, 2nd, 3rd, and 4th Affiliated Hospitals, College of Stomatology, College of Nursing, College of Health Management, Graduate School, College of Adult Education (College of Continuing Education), Department of Bioinfomatics, Department of Humanities and Social Sciences, Department of Sports, etc.

Also based at HMU are National Base for the Research of Basic Science and Teaching Talents Cultivation, Center for Endemic Disease Control of CDC, National Research Center for Clinical Trial of New Drugs, Russian Language Training Center of MOH, Heilongjiang Branch of Chinese Academy of Medical Sciences, Heilongjiang Academy of Medical Sciences, etc.