<p>Cross-border natural toponymic heritage (CNTH) carries significant implications for regional sustainable development, though its conservation and management face considerable institutional challenges. This study presents the first national-scale analysis of CNTH in China. Based on an inventory of 11,713 sites and employing spatial statistics and Geo-detector analysis, it reveals a highly clustered distribution, dominated by mountain-related toponyms and concentrated in southern China. The spatial pattern is primarily driven by moderate topographic complexity (elevation differences of 1000–2000 m), further shaped by historical corridors and administrative stability. The analysis demonstrates that this spatial clustering directly translates into systemic governance challenges, including fragmented legal statuses and asynchronous development across provincial borders, as illustrated by cases like Qiyun and Wuyi Mountains. In response, we propose a pragmatic governance framework that moves beyond technical solutions. Its core recommendations include establishing a pilot shared geospatial database in identified hotspots, developing tailored cooperative agreements for different CNTH typologies, and linking incentives to verifiable collaborative outcomes. The study concludes that sustainable CNTH management requires a fundamental shift from a technocratic to a problematized governance approach. This approach must explicitly address the political economy of inter-jurisdictional collaboration, positioning digital tools within a broader strategy to negotiate shared responsibility for fragmented heritage resources.</p>