Objective To analyze the mental health status and its influencing factors of navy crews during long-term sailing. Methods Totally 172 crews with long-term sailing were collected by random sampling method. The mental health status of the crews was assessed by Eysenck Personality Questionnaire (EPQ) and Symptom Checklist-90 (SCL-90) at 1 week before the long-term sailing (first assessment). The psychological measurement and investigation of crews was conducted by SCL-90, Fatigue Scale-14 (FS-14) and Assens Insomnia Scale (AIS) after 4-month long-term sailing (second assessment). The differences in the total score of SCL-90 and each factor scores of crews between the first assessment, the second assessment and the military norm were analyzed to determine the influence of long-term sailing on the mental health status of crews. The relationship between the total score of SCL-90 and each factor scores (second assessment) and AIS, FS-14, and EPQ were used to analyze the correlation of the mental health status of crew with sleep, fatigue and personality traits. The major factors influencing the mental health status of crews during long-time sailing were explored by multivariate linear regression analysis with the SCL-90 score as the dependent variable. Results The mental health status of crews after 4-month long-term sailing was significantly lower than that before the sailing, with significant difference in SCL-90 scores (P<0.01). The mental health status of crews was moderately correlated with personality traits, sleep, and fatigue (r>0.4, P<0.01). Multivariate linear regression analysis showed that neuroticism, seasickness, total score of sleep, total score of fatigue, working pressure, mental quality and ship adaptability were the major factors influencing the total score of SCL-90. Conclusion The long-time sailing on the sea has a bad influence on the mental health of navy crews. The seasickness, personality traits, working pressure, sleep, fatigue, and ship adaptability are the major factors influencing the mental health of crews.