Objective To explore the mental health status and influencing factors of clinical medical students pursuing a professional master’s degree under the “dual-track integration” training systems. Methods Clinical medical students pursuing a professional master’s degree who underwent residency standardized training in 123 hospitals from different areas of China were selected as the research objects from May 28th to June 4th, 2024, and the mental health and stress were investigated by questionnaire. Results A total of 1195 clinical medical students pursuing a professional master’s degree were included. Symptom Checklist-90 analysis showed that 582 (48.7%) master students had mental health problems. The two-group students (with and without psychological problems) had statistical differences in exercise frequency, sleep quality, extent of staying up late, interpersonal communication, and average number of night shifts per month (P<0.001). The subjective scores of interpersonal pressure, economic pressure, love and marriage pressure, schoolwork pressure, scientific research pressure, clinical work pressure, entering higher education pressure and employment pressure, and the proportion of graduating from 985/211 university of the master students with psychological problems were significantly higher than those of the master students without psychological problems (P<0.001). Logistic regression analysis showed that poor sleep quality [odds ratio (OR)=1.626, 95% confidence interval (CI) (1.085, 2.438), P=0.019], 985/211 university degree [OR=1.448, 95%CI (1.097, 1.910), P=0.009], interpersonal pressure [OR=1.194, 95%CI (1.121, 1.272), P<0.001], love and marriage pressure [OR=1.067, 95%CI (1.014, 1.122), P=0.012] and entering higher education pressure [OR=1.110, 95%CI (1.055, 1.167), P<0.001] were independent risk factors, while the male sex [OR=0.621, 95%CI (0.472, 0.817), P=0.001] were protective factor for psychological problems of these medical students. Conclusions Under the “dual-track integration” training systems, the clinical medical students pursuing a professional master’s degree have a higher prevalence of psychological problems, especially the females and the 985/211 bachelor’s degree scholars. It is important to improve sleep quality, strengthen interpersonal interaction and reduce pressure load to improve the mental health level of these clinical medical students.