Objective: To evaluate physical fitness status of medical college students using cluster analysis, to explore intercorrelations among of physical fitness indices, and to provide a theoretical basis for physical health training of medical colleges. Methods: Based on the 2014 revised Chinese National Student Physical Fitness Standard(CNSPFS), 10 431 undergraduates of Zhejiang Chinese Medical University in 2018 were recruited as participants, cluster analysis and category description were performed by using SPSS 21.0. Results: The two-step classification showed that medical college students were classified into three categories according to their physical fitness score: A, B, and C, which was 25.8%(1 165), 37.2%(1 169) and 37.0%(812) in male students and 32.4%(2 361), 50.8%(3 703) and 16.8%(1 221) in female students; the ranking of factors and based on specific contribution to physical fitness for males: BMI(1.00), standing long jump(0.98), pull-ups(0.88); females: BMI(1.00), 800 m(0.99), standing long jump(0.89). Conclusion Antropometric indicators play a key role in physical fitness among medical college students, and have a greater impact compared with other indicators; strength and endurance quality are the key factors to improve the performance of male and female physical fitness tests; It is of great significance for colleges and universities to carry out differentiated exercises plan for the rapid improvement of students’ physical fitness.