Abstract: Modernization of border governance, as a strategic fulcrum of the modernization of national governance capacity, has become a core proposition that runs through the overall situation of national security and development. This paper took Village M in the border area of Yunnan Province as the research object, and constructed an integrated analytical framework of “embedded governance - political potential” to reveal the mechanism of generating the effectiveness of the Party building leading the modernization of border governance. The research found that, the resolution of the governance predicament in border areas depended on the deep embedding of the Party organization at the structural, relational and cognitive levels, as well as the effective accumulation, transformation and release of political potential. The two work formed a “rigid and flexible” governance logic. On this basis, a theoretical model of “institutional effectiveness = embedding depth × potential intensity” was proposed to demonstrate the collaborative logic of the “rigid organizational foundation” and “flexible potential adjustment” in border governance.