Leveraging the inauguration of the China-Europe Railway Express (CRE) as a natural experiment, this study employs a multi-period difference-in-differences (DID) model using data from China’s listed manufacturing firms spanning 2011 to 2021. The findings reveal that the CRE has significantly enhanced the green innovation capabilities of manufacturing enterprises, with a notably stronger impact on substantive green innovation than strategic green innovation. These results are further reinforced through rigorous robustness checks, including instrumental variable approaches, propensity score matching combined with difference-in-differences (PSM+DID) regression, and variable substitution. The study identifies two primary mechanisms driving the CRE’s positive impact on corporate green innovation: alleviating financial constraints and facilitating cross-border innovation resource flows. Heterogeneity analysis indicates that the CRE’s benefits are particularly pronounced among non-stateowned enterprises, firms with lower degrees of internationalization, and smaller firms. Regionally, the impact is most substantial in the central regions, followed by the eastern regions, while the western regions show limited effects due to structural challenges. Industry-level analysis reveals a hierarchical impact, with high-tech manufacturing deriving the greatest benefit, followed by medium-tech and traditional manufacturing sectors. This study contributes theoretical insights and offers actionable policy recommendations to maximize the CRE’s potential in fostering green innovation, addressing regional inequalities, and advancing sustainable international trade and logistics.