Socio-ecological systems in basin regions characterized by diverse cultural traditions and hierarchical village spatial structure are undergoing profound transformation driven by multifunctional demands and spatial restructuring. This study develops an analytical framework encompassing economic production, socio-cultural functions, and ecological potential to examine the spatial differentiation and socio-ecological coupling mechanisms within the Yilong Lake Basin, Yunnan Province. Through the entropy weighting method and a coupling coordination model, the framework evaluates the “lake–mountain–village” gradient of spatial differentiation. The results indicate that: (1) the overall coordination level of multifunctional systems in the region remains relatively low, exhibiting a decreasing trend from lakeshore to the mountain periphery; (2) village-level dependencies of spatial functions can be summarized into three coupling categories—associated with institutional embedding, self-organization, and value mismatch—revealing distinct socio-ecological interaction patterns; and (3) three coupling categories correspond to three differentiated governance pathways, namely coupling optimization, functional transition, and conflict mitigation. The study advances theoretical and methodological insights into the spatial differentiation and evolution of complex village systems, highlighting the nonlinear coexistence of interdependence and constraint among economic, social, and ecological functions. It further provides practical guidance for coordinated governance and sustainable spatial planning in similar rural and basin environments worldwide.