Flipped classroom has received much attention in medical education. The aim of this study was to evaluate the efficacy of flipped classroom combing with human anatomy web-based learning system in anatomy education.A total of 89 freshmen in medical specialty were enrolled and randomly allocated into either the experimental group (receiving the flipped classroom with human anatomy web-based learning system, n = 45) or control group (receiving the traditional classroom teaching, n = 44). A pre-quiz and a post-quiz were conducted before and after the classes, respectively. The improvement in scores between groups was compared. A 5-point Likert scale questionnaire was used to evaluate perceptions and experience.The mean pre-quiz scores of the 2 groups were comparable (all P > .05). However, the mean post-quiz score in the experimental group was significantly higher than that in the control group (91.44 ± 6.25 vs 86.13 ± 11.67, P < .05). The results of questionnaires showed that 44 (97.8%) students agreed with flipped classroom combined with human anatomy web-based learning system, 43 (95.6%) students obtained improved study interest in anatomy learning, and 42 (93.3%) students felt that the interactive, applied in-class activities during the class greatly enhanced their learning.Flipped classroom combined with human anatomy web-based learning system can be used as an effective learning tool for anatomy education.