Abstract: As a strategic emerging industry prioritized in the national proposal for the 15th Five-Year Plan, the low-altitude economy offers a novel strategic pathway for the mountainous regions of Southwest China to overcome geographical constraints and reshape their development patterns. From the perspective of political economy, this paper constructed an analytical framework of “productivity–space–governance” to uncover the inherent logic and practical contradictions underlying the empowerment of the southwestern mountainous areas by the low-altitude economy, and to explore the construction of a compatible governance system, thereby providing theoretical support for coordinated regional development. Through spatial restructuring, the low-altitude economy compresses geographic time, activates three-dimensional resources, and extends public services and data elements, injecting new-quality momentum into the southwestern mountainous areas to remedy developmental shortcomings and integrate them into broader endeavor of coordinated regional development. However, its development faces three major practical contradictions: tensions between selective capital accumulation and coordinated regional development; the urgent need for coordination between unified national airspace security management and locally differentiated developmental demands; and potential conflicts between technology-driven efficiency orientations and community rights and ecological protection. To address these challenges, it is imperative to establish a three-dimensional collaborative governance system through systematic innovations such as multi-stakeholder consultation, targeted and differentiated policies, pilot projects for flexible airspace management, and local capacity building, so as to guide the low-altitude economy to truly become a lasting driver of high-quality development in the southwestern mountainous regions and provide solid support for common prosperity in these areas.