In order to ensure the transparency and openness of each link of agricultural products “from farmland to table” and to solve the problem of consumers’ low trust degree in the safety of agricultural products and food, the application and evaluation of agricultural Internet of Things traceability system are the top priority. However, the traceability system evaluation indicators are rarely discussed in the existing studies. Consequently, this paper attempts to construct the evaluation index system of the Internet of Things traceability system of agricultural products based on an overall perspective of ecological civilization and to determine the weight of each evaluation index by using analytic hierarchy process (AHP). Then, on the basis of the relevant data of the agricultural product traceability system in recent years, the determined weight is modified by using entropy method. Finally, it points out the important practical value for management departments, production subjects, sales subjects, and consumers, providing reference for improving the quality and safety of agricultural products and standardizing the market supervision of agricultural product market.