Objective To understand the current situation of healthcare-associated infection (HAI) and community-associated infection (CAI) in medical institutions in Wuhan City, and analyze the epidemic trend and key management of HAI. Methods The combination of medical record and bedside survey was adopted to conduct a survey according to the table of cross-sectional survey formulated by National HAI Monitoring and Management Training Base. Survey data from 2016, 2018, and 2020 were analyzed. Results HAI prevalence rates in Wuhan City in 2016, 2018, and 2020 were 2.66%, 2.21%, and 1.85%, respectively. CAI prevalence rates were 17.81%, 17.82%, and 16.29%, respectively. Both showed decreasing trends (both P < 0.05). Departments with high pre-valence rates of HAI were the intensive care unit (ICU), departments (groups) of hematology, neurosurgery, thoracic surgery, and pediatric neonatal. Departments with high prevalence rates of CAI were the departments (groups) of pediatric non-neonatal, respiratory diseases, infectious diseases, general ICU, and pediatric neonatal. The main infection sites of HAI and CAI were lower respiratory tract. The proportions of postoperative HAI at lower respiratory tract in 2016, 2018, and 2020 were 12.85%, 18.39%, and 22.09%, respectively. HAI rates at surgical site in 2016, 2018, and 2020 were 0.99%, 0.82%, and 0.69%, respectively. HAI and CAI were mainly caused by Gram-negative bacteria. Conclusion The management of HAI in medical institutions in Wuhan City in 2016, 2018, and 2020 have made achievements. However, infection control in general ICU and of HAI at lower respiratory tract still need to be strengthened and improved.