Logistics system evaluation is a key part of logistics system research and an important basis for logistics system decision-making. The process of evaluating logistics systems includes two key elements: the establishment of an evaluation index system and the selection of evaluation methods. Combined with the characteristics of the logistics system, taking into account the principles of systematization and practicability, this paper makes the following work. Firstly, through the analysis and screening of indicators, the evaluation index system of logistics system is constructed by using analytic hierarchy process, and secondly, a gray comprehensive evaluation model based on logistics system is established by using the gray correlation analysis theory, and finally the feasibility and effectiveness of the model are verified by combining with examples.