As a new trade format carrying “Internet + foreign trade”, the importance of cross-border e-commerce in improving supply chain efficiency and ensuring supply chain security has become increasingly prominent. Taking the policy of cross-border e-commerce comprehensive pilot area as a quasi-natural experiment, using the data of listed companies in China from 2008 to 2021 and a staggered difference-in-difference approach, this paper systematically examines the impact of cross-border e-commerce development on supply chain efficiency from the perspective of enterprise inventory.The research finds that the development of cross-border e-commerce significantly increases the inventory turnover rate of enterprises, thereby improving the efficiency of the supply chain. This conclusion is still valid after considering a series of factors that may interfere with the estimation results. The main channels for the reform of cross-border e-commerce to improve the efficiency of the supply chain include helping enterprises expand overseas markets, reducing demand uncertainty and promoting the integration of manufacturing and services industries. In addition, the construction of regional information infrastructure and the improvement of the institutional environment have further strengthened the role of cross-border e-commerce reform in the improvement of supply chain efficiency. Under the current background of China’s vigorous construction of cross-border e-commerce comprehensive pilot zones, the research conclusions of this paper provide policy implications for how to enhance the modernization level of the supply chain.