Objective To investigate and analyze the difficulties of nosocomial infection management in different-level medical institutions in Shanghai, and to provide scientific basis for improving the level of nosocomial infection management. Methods A questionnaire was designed to include 10 difficulties in nosocomial infection management such as professional title promotion, salary, and personnel allocation. In October 2023, the Shanghai Nosocomial Infection Quality Control Center, in collaboration with the Shanghai Hospital Association, conducted a questionnaire survey among the heads of nosocomial infection management departments in medical institutions in Shanghai. The scores of difficulties were analyzed by stratification according to hospital level, allocation and changes of full-time personnel. Results A total of 548 questionnaires were distributed, and 530 valid questionnaires were retrieved, with a recovery rate of 96.72%. There were 55 public tertiary, 93 public secondary, 169 public primary and 213 social medical institutions. The rates of full-time personnel allocation meeting standards were 76.36% (42/55), 72.04% (67/93), 31.95% (54/169), and 21.60% (46/213), respectively. There was a statistically significant difference in the rates of full-time personnel allocation meeting standards among different levels of medical institutions (χ2=105.149, P<0.001). There was no statistical difference in the total scores of nosocomial infection management difficulties among different-level medical institutions (F=1.657, P=0.176). There were statistically significant differences in the scores of difficulties in professional title promotion, cumbersome daily norms and requirements, insufficient allocation of full-time personnel, and high personnel turnover (P<0.05). Conclusions The main difficulties in nosocomial management of medical institutions at all levels in Shanghai include the difficulty in career promotion, cumbersome daily norms and requirements, insufficient allocation of full-time personnel and lack of experience. In the future, medical institutions should strengthen the allocation of full-time personnel and enhance their capabilities, provide smooth promotion channels, to promote the high-quality development of nosocomial infection management ultimately.