After the occurrence of public health emergencies, due to the uncertainty of the evolution of events and the asymmetry of pandemic information, the public’s risk perception will fluctuate dramatically. Excessive risk perception often causes the public to overreact to emergencies, resulting in irrational behaviors, which have a negative impact on economic development and social order. However, low-risk perception will reduce individual awareness of prevention and control, which is not conducive to the implementation of government pandemic prevention and control measures. Therefore, it is of great significance to accurately evaluate public risk perception for improving government risk management. This paper took the evolution of public risk perception based on the COVID-19 region as the research object. First, we analyze the characteristics of infectious diseases in the evolution of public risk perception of public health emergencies. Second, we analyze the characteristics of risk perception transmission in social networks. Third, we establish the dynamic model of public risk perception evolution based on SEIR, and the evolution mechanism of the public risk perception network is revealed through simulation experiments. Finally, we provide policy suggestions for government departments to deal with public health emergencies based on the conclusions of this study.