In recent years, people pay more and more attention to food safety. In order to study the relationship between agricultural product safety and location selection of distribution centers, this paper studies the establishment mechanism of agricultural product distribution centers based on food safety in the e-commerce environment. Based on the cost optimization perspective, the analytic hierarchy process is used to qualitatively analyze the four influencing factors of transportation cost, storage cost, processing cost and human resource cost, and the relevant weights are obtained. Then the gray correlation degree is used to evaluate the four candidate towns. The selection of the optimal distribution center site is selected to provide reference for the research of fresh and perishable products such as yak meat, and the research on the safety mechanism of agricultural products is put forward.