This research was aimed at exploring the construction and evaluation method of the comprehensive emergency response system for public health emergencies under the COVID-19 (coronavirus disease 2019) epidemic situation based on discrete stochastic mathematical model. The response of the Centers for Disease Control and Prevention (CDCP) of Taiyuan city in the COVID-19 epidemic situation was taken as an example. A new discrete stochastic COVID-19 epidemic spread mathematical model which integrated public health intervention and input cases was proposed. The model was parameterized by multisource data, and the impact of different flow patterns on the risk of secondary outbreak was analyzed. The advantages and disadvantages of its emergency system construction were analyzed. Additionally, the improvement measures and suggestions for the existing problems were proposed. Results suggested that there was only one specialized disease prevention and control institution in Taiyuan, and there were only 11 centers for disease prevention and control, accounting for 6.2% (11/177) of the total in Shanxi Province. Through the analysis, it was found that the current public health emergency response system in Taiyuan city had imperfect management coordination mechanism, incomplete plan type, serious shortage of public health personnel, poor information communication efficiency, insufficient early warning efficiency of the epidemic detection system, and weak logistics material security links. Therefore, it was proposed to establish a sound coordination system of emergency health management and vigorously promote the construction of emergency health management institutions. Thus, a public health emergency management system integrating management coordination system, plan system, emergency team building system, material reserve management, and other functions was formed. The application of discrete stochastic mathematical model suggests that intermittent population flow and effective isolation of infected people in transient population can effectively reduce the risk of secondary outbreak. The system analysis here also provides theoretical basis for improving the construction of public health emergency response system in Taiyuan.