Based on industrial integration theory and system theory, this paper combines the development characteristics of e-commerce and cross-border logistics, utilizes the entropy weight method to assign weights to the indicators, and constructs a comprehensive evaluation model of e-commerce and cross-border logistics. Measure the coupling degree and integration degree of e-commerce and cross-border logistics. Using the multiple regression method to comprehensively study the technique of variable correlation and the important measures of the link between each variable, thus put forward optimization strategies for the logistics supply chain model, enterprise scale, and other aspects. The results of the analysis show that the proportion of cross-border e-commerce import transaction scale reached 22.7% in 2023, which increased 1.29 times compared with 2019, and the proportion of cross-border e-commerce import transactions continued to increase. In the analysis of the factors of the industrial integration of e-commerce and cross-border logistics, the influence of information network technology (0.108), the influence of platform resources, and the degree of influence of manufacturing technology occupy the top 3 places, which are the elements to focus on. Enterprise performance is significantly impacted by the economic level of the host province through regression analysis, with a coefficient of 0.1847 and significant at the 10% level. The evaluation value of the logistics alliance model is the best (comprehensive evaluation of 0.384), and it is most in line with the current development needs of cross-border e-commerce companies.