Objective To discuss the effect of applying special investigation on the hand hygiene compliance and knowledge of medical staff in key departments combined with nosocomial infection information system in reducing nosocomial infections. Methods A total of 527 patients admitted to the key departments from January 2018 to December 2020 were selected, and were grouped according to the time of admission.The control group received routine nosocomial infection management, and the observation group received the management based on nosocomial infection information system.A special survey of hand hygiene compliance and related knowledge was carried out on 100 medical staff in those department, and the differences in hand hygiene compliance, hand hygiene knowledge and nosocomial infection rates between the two groups were compared. Results The hand hygiene compliance and hand hygiene knowledge scores of the medical staff in the observation group were significantly higher than those in the control group (P<0.05). The infection rate of observation patients was lower than control patients (P<0.05). Conclusions The use of special survey on hand hygiene compliance and knowledge of medical staff in key departments combined with nosocomial infection information systems can effectively improve medical staff's hand hygiene compliance and related knowledge, reduce the risk of nosocomial infections, which is worthy of promotion.