Objective To investigate the current status of healthcare-associated infection (HAI) management in medical institutions in Shanghai, analyze the implementation of HAI surveillance indicators, and provide evidence to support the improvement of refined and scientific HAI management. Methods Using the Shanghai Three-Network Linkage Platform, a survey was conducted from April to May 2025 covering HAI management practices in the preceding year at medical institutions in Shanghai. Investigation and analysis were conducted on the HAI information systems, staffing of infection prevention and control (IPC) professionals, and implementation of HAI surveillance indicators. Results A total of 56 medical institutions in 16 administrative districts of Shanghai were surveyed. Among them, there were 45 tertiary medical institutions and 11 secondary medical institutions. There were 48 comprehensive medical institutions and 8 specialized medical institutions. All 56 medical institutions had established fully functional HAI information systems (100.0%). The structure and training compliance of IPC personnel were generally satisfactory; however, 4 institutions (7.1%) had insufficient IPC staffing levels. No statistically significant differences were observed between tertiary and secondary hospitals in the scores for implementation of HAI surveillance indicators (P>0.05). In contrast, significant differences were found between general and specialty hospitals in scores for rates of three types of device-associated infections (P=0.005) and hand hygiene compliance (P=0.041). After standardization of indicator implementation scores, the five lowest-scoring indicators requiring priority attention were, in descending order: blood culture submission rate for patients with pneumonia and fever ≥38.5°C; blood culture submission rate for patients with central venous catheters retained for ≥5 days; timing of perioperative prophylactic antimicrobial use for Class Ⅰ surgical incisions; catheter-related urinary tract infection incidence; and consumption of liquid soap and alcohol-based hand rub in wards. Conclusions Overall, HAI information system construction and management frameworks in Shanghai medical institutions are well established and functioning effectively. Nevertheless, gaps remain in IPC staffing allocation and in the clinical implementation of certain core HAI surveillance indicators. Continued efforts are required to advance the standardization and refinement of HAI management.