Under the President level, it is divided into Academic Divisions, Administrative Divisions, Affiliated Hospitals and Units.
There are 8 units below the Academic Divisions level
- College of Medicine
- College of Dental Medicine
- College of Pharmacy
- College of Nursing
- College of Health Sciences
- College of Life Sciences
- College of Humanities and Social Sciences
- Center for General Education
There are 12 units below the Administrative Divisions level
- Office of Research and Development
- Office of Academic Affairs
- Office of Student Affairs
- Office of General Affairs
- Office of Library and Information Services
- Office of Global Affairs
- Office for Operation of Industry and University Cooperation
- Auditing Office
- Office of Secretariat
- Human Resources Office
- Office of Accounting
- Office of Environmental Safety and Health
There are 7 units below the Affiliated Hospitals and Units level
- Chung-Ho Memorial Hospital
- KMU Gang-Shan Hospital
- Kaohsiung Municipal Hsiao-Kang Hospital
- Kaohsiung Municipal Ta-Tung Hospital
- Kaohsiung Municipal Cijin Hospital
- Preschool
- After-School Child Care Center