In recent years, the frequent occurrence of public health emergencies has affected people’s daily lives. In response, this paper evaluates the risk of logistics terminal distribution and puts forward the corresponding countermeasures. Firstly, this paper summarizes relevant literature and analyzes the characteristics of public health emergencies and logistics terminal distribution. This paper constructs the risk index system of logistics terminal distribution under public health emergencies for the first time. Secondly, this paper conducts a questionnaire survey on a domestic e-commerce enterprise. In this paper, the intuitionistic fuzzy entropy weight method is applied to the obtained data to determine the weight of risk index. Finally, this paper adopts the grey fuzzy comprehensive evaluation method to evaluate the risk index of logistics terminal distribution under public health emergencies. This paper takes the impact of public health emergencies into account for the risk of logistics terminal distribution for the first time. Some suggestions are provided for preventing the logistics terminal distribution from stagnation and paralysis when public health emergencies occur. This paper supplements the existing research in this field.