Objective To investigate the mental health status of military healthcare workers in shelter hospitals in Shanghai during the epidemic caused by severe acute respiratory syndrome coronavirus 2 omicron variant and its influencing factors. Methods A total of 540 military healthcare workers in shelter hospitals in Shanghai were investigated with patient health questionnaire-9 (PHQ-9), generalized anxiety disorder-7 (GAD-7) and Athens insomnia scale (AIS) to explore their mental health status, and logistic regression was used to analyze the influencing factors. Results A total of 536 valid questionnaires were collected, with an effective rate of 99.3% (536/540). The incidence of depression, anxiety and insomnia among military healthcare workers in shelter hospitals in Shanghai was 45.5% (244/536), 26.1% (140/536) and 59.5% (319/536), respectively. Logistic regression analysis showed that whether people resided in Shanghai, the proportion of negative information in daily browsing information and diet status in shelter hospitals were the influencing factors of depression, anxiety and insomnia (all P<0.05); age and confidence in the future of Shanghai were the influencing factors of depression and insomnia (all P<0.05); and the time spent daily on epidemic-related information was an influencing factor of insomnia (P=0.021). Conclusion The incidence of depressive, anxiety and insomnia among military healthcare workers in shelter hospitals in Shanghai is high during the epidemic caused by severe acute respiratory syndrome coronavirus 2 omicron variant. Psychological consequences of the epidemic should be monitored regularly and continuously to promote the mental health of military healthcare workers.