In the dynamic model of infectious diseases, the use of traditional methods to estimate the number of incidence, there is often a theoretical analysis of high complexity, immediacy and poor. The nonlinear dynamic model of the observer in the incidence of infectious diseases estimation method can better solve the problem. This paper presents a nonlinear observer on the incidence of infectious disease dynamics model estimation method. System dynamics model for infectious diseases have incubation period, the structure of the corresponding nonlinear systems observer, the observer for nonlinear systems to predict the number of cases. The present invention is not only simple, can be estimated coefficient estimates and infectious disease incidence rate, but also on other parameters such as illness mortality and recovery rates can also be estimated and the adaptability and accuracy have certain advantage of the prevention and control of infectious diseases actually have some reference value.