With the improvement of environmental awareness, green logistics, as a kind of logistics mode that can realize the unity of economic benefits and environmental benefits, has been paid more and more attention by the academia and the industry. However, how to effectively evaluate the operation effect of green logistics is still a problem to be solved. To solve this problem, this paper proposes a green logistics evaluation index system based on factor analysis, and verifies its effectiveness through simulation data. In the process of building and validating the model, rigorous mathematical modeling methods were used, combined with a large number of actual data. The results show that the evaluation index system of this study can accurately predict the operation effect of green logistics, and provide a practical evaluation tool for enterprises. Finally, the model is optimized to further improve its prediction accuracy. This study is of great significance to theoretical research and practical application.