Objective To analyze the influencing factors of medical students' selection of overseas exchange programs, and propose recommendations to promote medical students' participation and strengthen international talent training. Methods In February and March, 2023, a questionnaire survey was conducted for students from Peking University Health Science Center who had participated or intended to participate in overseas exchanges programs, χ² test was used to compare influencing factors affecting the selection of these programs and preferences of program features by medical students of different educational levels and genders. Results A total of 1 158 valid questionnaires were collected. The influencing factors with proportion of importance ranked top 3 in medical students' selection of overseas exchange programs were host universities' education quality [1 073 (92.7%)], school reputation [1 045 (90.2%)], and public security/personal safety [1 043 (90.1%)]. In addition, the following influencing factors such as the reputation of the supervisors [999 (86.3%)], difficulty in application [871 (75.2%)], international environment [856 (73.9%)], and program cost [816 (70.5%)] were all above 70%. There were statistically significant differences among students of different educational levels in relation to the proportion of importance of factors such as location of overseas exchange programs, campus facility and logistics support, and program duration (all P<0.05). For example, compared with undergraduate students [368 (52.5%)] and master students [125 (61.9%)], a higher proportion of doctoral students [168 (65.9%)] believed that the impact of program duration is important. Male and female medical students differed in the proportion of importance of factors such as international environment and academic pressure (all P<0.05). For example, compared with male students ([345 (70.1%)], a higher proportion of female students [511 (76.7%)] believed that the impact of international environment is important. Conclusions Medical students' selection of overseas exchange programs is mainly affected by program quality, safety, difficulty in application, and program cost. There are differences in the preferences of overseas exchange program features by medical students of different educational levels and genders. Therefore, when carrying out overseas exchange programs for medical students, the school should focus on the quality and safety of the programs, provide students with support in application procedures and program costs, develop different types of programs for different student groups.