The article firstly constructs a comprehensive evaluation index system for the two systems of cross-border e-commerce and cross-border logistics, and then conducts an empirical analysis of the coupling coordination level based on the data samples of cross-border e-commerce and cross-border logistics in Chongqing city from 2016-2021 by using the entropy value method and the coupling coordination degree model comprehensively. The research results show that the overall comprehensive development levels of the two subsystems of cross-border e-commerce and cross-border logistics in Chongqing show a year-on-year increasing trend, with the comprehensive development level of the cross-border e-commerce subsystem increasing from 0.11603 to 0.94001 and the comprehensive development level of the cross-border logistics subsystem increasing from 0.07472 to 0.85057. The coupling coordination level of the two systems increases from 0.21577 in 2016 to 0.85057 in 2021. 0.21577 to 0.66865 in 2021, and the coordination level has transitioned from moderate dysfunctional recession to primary coordinated development stage.