Objective To investigate the current status of infection control of coronavirus disease 2019 (COVID-19) in hospitals of different levels, providing strategies and suggestions for occupational infection prevention. Methods The frontline health workers of hospitals of different levels were selected to finish the questionnaire survey by WeChat from Mar. 2 to 9, 2020. The questionnaire was designed with “questionnaire star”, including the basic information of health workers, the protection knowledge, the working environment against the epidemic, the management of medical protective products and the implementation of protective measures. Results A total of 966 valid questionnaires were collected and filled out by the health workers of nine tertiary hospitals and 42 community health service centers (CHSCs) in 15 districts of Shanghai. The training rate of COVID-19 epidemic protective knowledge in CHSCs was higher than that in tertiary hospitals (90.45% [644/712] vs 79.53% [202/254]), the difference was statistically significant (χ²=20.528, P=0.001). CHSCs had better COVID-19-related knowledges of identifying the corresponding categories of patients (χ²=27.108, P=0.009), hand disinfection, wearing and taking off protective clothing (χ²=22.666, P=0.001), and correctly managing medical waste (χ²=74.251, P=0.001). During the implementation of COVID-19 protective measures, the proportion of the CHSCs that could change disposable protective clothing strictly according to needs and protection intensity was significantly higher than that in tertiary hospitals (31.74% [226/712]) vs 25.20% [64/254]) (χ²=33.229, P=0.001). However, there were no statistically significant differences in the correct implementation of patient specimen collection, the frequency of changing protective mask, and working hours in hospital every week during the epidemic (all P>0.05). Conclusion CHSCs play an important role in the prevention of the COVID-19 epidemic. There are differences in some measures of epidemic prevention between CHSCs and tertiary hospitals. It is necessary to further improve the measures to reduce the risk of COVID-19 occupational infection in the medical institutions.