Abstract Background There have been very few studies analyzing the relationship of physical and mental health status with health behaviors and deployment status in Chinese navy personnel. Thus, we undertook this survey to assess this relationship and identify specific factors affecting the physical and mental health status. Methods The subjects enrolled in this study were selected from four units of the active-duty navy personnel in China, based on a cluster random sampling design. A total of 1200 Chinese navy personnel participated and completed the questionnaire survey that included veteran SF-36 form and a self-designed questionnaire regarding their sociodemographic characteristics, deployment status, self-rated health status and health behaviors. Totally 1200 questionnaires were distributed to different participants, while 1083 valid questionnaires were included in the final analysis. All data were analyzed using SPSS18.0 software. Results Based on the information provided by navy personnel, 17.82, 35.09 and 23.08% rated their health as excellent, very good and good, respectively. The mean score of physical component summary (PCS) and mental component summary (MCS) was 50.53 and 41.39, respectively. Length of service, binge drinking, regular drinking and BMI appeared to be associated with PCS score, while household income, binge drinking and BMI affected MCS score. Deployment status and smoking exhibited no significant association with PCS and MCS scores. Conclusions Our study suggested that the sociodemographic factors like length of service and household income, along with behavioral risk factors like binge drinking, regular drinking and body mass index (BMI), seem to affect the physical and mental health status of Chinese navy personnel. However, additional data collection and more detailed analysis would still be required to develop a systematic, comprehensive and corresponding health education program to promote overall health status.