Objective To investigate the relationship between stress and social anxiety of medical students in military universities, and to explore the related mechanisms. Methods Two hundred and eleven military medical university students were tested by interaction anxiousness scale (IAS), stress scale for college students (SSCS) and Connor-Davidson resilience scale (CD-RISC). The Pearson correlation analysis and structural equation model were used to analyze the relationship between the variables. Results A total of 198 valid questionnaires were collected, with the effective rate being 93.8%. There were significant correlations between social anxiety and various dimensions of stress and resilience (all P<0.01). Structural equation model showed that the resilience partially mediated the relationship between stress and social anxiety (χ²/df=2.08, P<0.05; root mean square error of approximation=0.074, comparative fit index=0.98, normed fit index=0.97, incremental fit index=0.98). The total stress score of the male students was greater than that of the female students in military medical universities (24.67±15.01 vs 20.17±13.07, t=2.17, P<0.05). Conclusion Resilience has partial mediating effect on the relationship between stress and social anxiety. Therefore daily management of military medical university students should be emphasized on the cultivation of resilience.