In the post-moderately prosperous era, rural revitalization faces a “disembedding” phenomenon involving three governance mechanisms—hierarchical, market, and community—where single governance mechanisms develop excessively and partially detach from the governance system, leading to governance imbalance. Based on Polanyi’s concept of “disembedding,” this study constructs an analytical framework for the disembedding and co-embedding of governance mechanisms, and explores the complex process of rural governance system transformation through three typical village cases. The research findings reveal that: hierarchical mechanism disembedding manifests as alienation of public values, rigidification of decision-making models, and development path dependency; market mechanism disembedding shows as expansion of economic rationality, collective action dilemmas, and industrial development bottlenecks; community mechanism disembedding presents as solidification of traditional bonds, clan fragmentation, and constrained development. The co-embedding of rural governance mechanisms is achieved through proactive early intervention under meta-governance by higher-level governments, realizing dynamic embedding of hierarchical, market, and community governance mechanisms while avoiding severe disruptions during the transformation process, thus forming an “anticipatory embedding” model rooted in the Chinese context.