The development and expansion of a new type of rural collective economy is an important measure to promote the comprehensive revitalization of the countryside, the modernization of agriculture and rural areas, and the common prosperity of farmers and rural areas. This study takes District Y of City X, which is located in an underdeveloped area, as a case study, systematically combs through the evolution of the rural collective economy, focuses on the exploration of the practice of "separation of politics and economy" in the pilot area and its operation logic and carries out an in-depth exploration of it, and builds an analytical framework of pluralistic co-governance based on the theories of "system-resource-technology" and autonomous governance, so as to analyze the mechanism of the occurrence of the practice of "separation of politics and economy" and the mechanisms for enriching and developing the villages. The results of this study show that through the "separation of politics and economics", villages are able to realize the market-oriented operation of the rural collective economy in accordance with their own endowments, which has the characteristics of clarifying the boundaries of the governance system, improving the efficiency of resource allocation, and promoting the collaborative governance of multiple subjects. This can effectively boost the operating income of the rural collective economy, gradually build a solid foundation for factor interaction, strengthen the consensus of the interests of multiple governance actors, and promote the realization of high-quality development of the rural collective economy. However, there are still common problems in the development of the new rural collective economy, such as a weak development foundation, an unsmooth system operation mechanism, and a weak capacity of the main body of governance. Therefore, this study gives path optimization strategies from optimizing the top-level design, innovating the institutional mechanism, cultivating the development momentum, and strengthening the support of factors.