With the development of the market economy, new farmers’ cooperative economic organisations have flourished, and with their organisational appeal, linkage of economic interests and attraction, they have brought together and driven a large number of farmers, accumulated rich social capital, become the emerging subjects of rural governance, and influenced and changed the existential ecology of rural governance. Based on the perspective of new farmers’ cooperative economic organisations, this paper provides a relatively comprehensive and systematic exploration of rural governance embedded in new farmers’ cooperative economic organisations with the help of coordination theory, institutional theory and the utility function in calculus theory. The specific operation, motivation, and guarantee mechanisms under the organization’s participation in rural governance are empirically examined. The mean value of the composite index of the level of rural governance under the participation of NPCE organisations is 0.633, with a coefficient of variation of 0.144. It is found that the participation of the new farmers’ cooperative economic organisations in rural governance is a stage-by-stage development trend. In the long run, rural governance will eventually shift to a pattern of multiple co-governance, led by the market, guided by the government, and directed by village organizations.