Objective To analyze the influencing factors affecting the self-efficacy of medical master's degree students and to inform future improvement of the quality of online education. Methods A national survey on the educational satisfaction of recent medical graduate students was conducted from June to July 2022, in which 6 704 medical master's degree students from 49 institutions with online class experience were enrolled. The t-test and ANOVA were used to compare the differences in personal characteristics of self-efficacy, online learning engagement and external support self-assessment scores; and multiple linear stepwise regression was used to analyze the influencing factors of self-efficacy of medical master's degree students. Results The self-efficacy score of medical master's degree students was (3.81±0.96), the online learning engagement score was (4.00±0.95), and the external support score was (4.27±0.83). There was a positive correlation between self-efficacy, online learning engagement and external support of medical master's degree students (all P<0.001). Online learning engagement (β=0.53, P<0.001) and external support (β=0.16, P=0.008) were the influencing factors of self-efficacy among medical master's students. Conclusions The self-efficacy of medical master's degree students needs to be improved, and the online learning input of medical master's degree students can be promoted through the development of effective teaching measures, the enhancement of teacher-student interaction, and the provision of external support to improve self-efficacy, and then improve the quality of online education.