Farmer cooperatives play a significant role in increasing farmers’ income, ensuring food security, and maintaining supply chain stability. While the number of cooperatives in China has increased rapidly in recent years, it is challenge for many small-scale cooperatives in China to achieve high performance due to resource and scale constraints. Taking Rui’an Meiyu’s Trinity Comprehensive Cooperation Organization as an example, this paper makes improvement to the original Trinity Comprehensive Cooperation Model and innovatively proposes a new practicable model called “three areas of cooperation with multiple bodies” for small-scale cooperatives to adopt. According to our research, the following features have been identified: first, the formation motivations of the new model include four different aspects, and the formation process of it includes three specific steps. Second, the resource integration mechanism of the new model is composed of production coordination optimization, supply and marketing platform restructuring, and credit capital guarantees. Third, the new cooperative model can increase economic benefits and simultaneously promote sustainable agricultural development. This study further complements the literature on the Trinity Comprehensive Cooperation Model and offers many managerial and academic implications for cooperative members and policy-makers.