Background With the dramatic growth in smartphones, mobile health applications (apps) in the field of healthcare or medicine, which are characterized by strong operability, flexibility and interactivity, provide a supplementary approach to medical learning. The aims of this study were to awaken medical students to pay more attention to the learning function of mobile health app and gain deeper insight into our understanding of the factors influencing medical students’ mobile health apps continuance intention for enhancing practical utilization. Methods A cross-sectional survey was conducted with a self-designed questionnaire administered to medical students at Chongqing Medical University. Data were collected from 450 participants from March to April 2019. SPSS V.25 was used for the descriptive statistical analysis of the results. Smart PLS 3.2.7 was used to construct a structural equation modelling framework to estimate the influencing factors of medical students’ continuance intention to use mobile health apps. Results The external characteristics of mobile health apps had a positive influence on perceived ease of use (β = 0.378, P < 0.001). Perceived ease of use had a positive impact on perceived usefulness (β = 0.573, P < 0.001). Perceived ease of use (β = 0.195, P = 0.011), perceived usefulness (β = 0.450, P < 0.001) and subjective norms (β = 0.255, P < 0.001) had a positive impact on attitude towards using mobile health apps. Additionally, perceived usefulness (β = 0.202, P < 0.001) and attitude (β = 0.730, P < 0.001) had a remarkable influence on continuance intention. Furthermore, the mediating effect of attitude between perceived usefulness and continuance intention was significant (β = 0.329, P < 0.001). Conclusion Both perceived usefulness and attitude have a significant effect on medical students’ mobile health apps continuance intention. So, we suggest apps providers and developers evoking and maintaining users’ interest in mobile health apps and perfecting apps’ features from various aspect. Also, more attention should be paid on social relationship to introduce medical students to familiarize mobile health apps and strengthen adhesiveness of medical students.