The cross-border e-commerce comprehensive pilot zone is an important measure for China to promote “institutional opening”, which plays a leading role in accelerating the deep integration of industrial and trade digitization, and in assisting the transformation and upgrading of traditional industries. At the same time, digital technology innovation provides new ideas for enterprises to promote digital transformation, enhance production efficiency, and increase market value. With the accelerated integration of the digital economy and the real economy, the role and mechanism of cross-border e-commerce in promoting digital technology innovation deserve further attention. Therefore, exploring the role and impact mechanism of cross-border e-commerce reform on digital technology innovation of micro-enterprises is of great significance for how to further improve the policy of opening up to the outside world and promote high-quality economic development. Additionally, as digital technology has broader development prospects and application value, the impact and mechanism of cross-border e-commerce development on digital technology innovation of enterprises deserve further exploration. This article uses a sample of A-share listed companies from 2007 to 2020 and treats the establishment of cross-border e-commerce comprehensive pilot zones as a quasi-natural experiment. Using a multi-period difference-in-differences model, it empirically explores the impact of cross-border e-commerce reform on digital technology innovation of export enterprises and its mechanism. The research results indicate that: firstly, cross-border e-commerce reform significantly enhances the level of digital technology innovation of export enterprises. After a series of robustness tests such as parallel trend tests, placebo tests, and replacement of explained variables, this conclusion still holds. Secondly, mechanism analysis finds that optimizing internal governance, reducing corporate financing and operating costs, and enhancing human capital are potential paths for cross-border e-commerce reform to promote digital technology innovation. Finally, heterogeneity analysis shows that the role of cross-border e-commerce reform in enhancing digital technology innovation mainly exists in enterprises with high financing constraints, strong environmental uncertainty, poor ESG performance, and relatively high human capital density in their regions. The marginal contributions of this article are mainly reflected in the following aspects. Firstly, in terms of research perspective, this article evaluates the impact of cross-border e-commerce comprehensive pilot zones on digital technology innovation of micro-enterprises for the first time, expanding the research perspective for evaluating the economic consequences of cross-border e-commerce reform. At the same time, it provides useful insights for further improving enterprise innovation incentive policies and enhancing the economic effect of cross-border e-commerce reform. Secondly, in terms of research methods, this article treats the establishment of cross-border e-commerce comprehensive pilot zones as a quasi-natural experiment and uses a multi-period difference-in-differences model to examine the impact and internal mechanism of cross-border e-commerce reform on digital technology innovation of enterprises, trying to overcome potential endogeneity problems in regression estimation processes. Finally, in terms of research content, this article analyzes and tests the impact mechanism of cross-border e-commerce reform on digital technology innovation of enterprises, deepening the understanding of the economic consequences of cross-border e-commerce reforms.