Objective To investigate the application of risk assessment in the control of nosocomial infections in surgical departments of infectious disease hospitals so as to provide references for the regulation of prevention and control measures. Methods Nosocomial infection risks in surgical departments of infectious disease hospitals were identified by the method of brainstorming. Based on risk assessment and planning of American children's national medical center in Washington for epidemic and infectious diseases control, the matrix method was used for risk assessment. The three highest risks were controlled, and then we compared the incidence of nosocomial infections before and after the risk assessment. Results The major risk factors in surgical departments existed in the process of diagnosis and treatment. By matrix scoring, excluding high readiness items, we found that the top three risks were airborne diseases, prevention and nursing of hematogenous infections and air disinfection. Nosocomial infection rate in the surgical departments dropped to 2.03% after carrying out risk assessment and taking correspondent measures (χ2=5.480,P=0.019). Conclusion Evaluation of nosocomial infection risk in surgical departments of infectious disease hospitals can discover major potential risks and reduce the incidence of nosocomial infections, which can provide references for management and control of nosocomial infections.