Objective To investigate the mental health status of naval officers and soldiers and its influencing factors, and explore the mediating effect of negative automatic thoughts on the relationship between psychological stress and mental health. Methods A total of 642 naval officers and soldiers from a naval force were investigated with the psychological stress self-evaluation test (PSET), the automatic thoughts questionnaire (ATQ) and the symptom checklist 90 (SCL-90), and the relationships between the variables were analyzed. Results Altogether 583 valid questionnaires were collected, with an effective rate of 90.80%. Correlation analysis showed that the degree of psychological stress and negative automatic thoughts were positively correlated with mental health (total score of SCL-90) (both P<0.05). Regression analysis showed that the degree of psychological stress and negative automatic thoughts could predict the mental health status; the mediating effect of negative automatic thoughts between the degree of psychological stress and mental health was significant (accounting for 37.30% of the total effect), and there were significant differences in mental health status among officers, sergeants and conscripts (P<0.05). Conclusion The degree of psychological stress and the negative automatic thoughts are important factors affecting the mental health of naval officers and soldiers. The degree of psychological stress can directly or indirectly affect the mental health through the mediating effect of negative automatic thoughts.