Economic globalization together with the extensive application of network technology has greatly accelerated the expansion of cross-border e-commerce in border regions, highlighting the practical significance of raising the standard of trade facilitation. This study seeks to assess the influence of trade facilitation on the export performance of cross-border e-commerce in frontier areas and to provide an objective evaluation of the level of trade facilitation across Chinese provinces. Four dimensions, regulatory environment, protective environment, customs environment, and e-commerce environment, are incorporated into an indicator framework for trade facilitation. An entropy-weight approach is employed to estimate provincial trade-facilitation levels in China from 2001 to 2021. The global Moran’s I index is then used to examine temporal evolution and spatial distribution patterns, while the entropy method is further applied to determine indicator weights. At the same time, the FE fixed-effects model, together with bilateral trade costs, is used to identify how trade facilitation affects cross-border e-commerce exports in China’s border regions. The empirical findings indicate that the overall level of trade facilitation in China has been rising steadily and in a favorable direction. Meanwhile, significant positive spatial agglomeration is observed, as reflected in a global Moran’s I value of 0.552. The results also show that every 1% increase in trade facilitation raises cross-border e-commerce exports in border regions by 0.825%, with bilateral trade costs playing an important mediating role. This study enriches the existing literature and provides more precise policy guidance for promoting the growth of cross-border e-commerce in frontier regions.