Objective To explore the influence of long-term navigation on mental health in warship crews, and to provide basis for making corresponding countermeasures. Methods All the personnel on a warship were selected by random cluster sampling when they had a long-term navigation. The Symptom Checklist-90 and Brief Cope questionnaire were carried out to collect data and the relationship between mental health and both coping style and individual factors was analyzed. Results Mental health state changed at early stage of ocean-going navigation, and there were significant correlation between the mental state index and the active coping strategies. Mental health state indexes did not return to normal level at the end of navigation. Indexes of mental health showed no significant difference between different educational backgrounds, marriage status and mental health factors. Regression analysis showed that self-efficacy was the important predictive index of mental health. Conclusions Ocean-going navigation has influence of the crew's mental health. More attention should be paid to those who have adopted negative coping style to cope with mental problems, and have low-level self-efficacy. Necessary psychological intervention should be given to the personnel who have just completed their long-term navigation to help them solve the mental health problems.