Abstract: “Large country with small-scale farming” is the basic national condition of agricultural production in China. How to effectively resolve the contradiction between the scattered operation of small-scale farmers and modern agriculture and the large market is the core issue in promoting agricultural modernization and achieving common prosperity. As the core carrier connecting small-scale farmers and the large market, farmers’ professional cooperatives play a crucial role in integrating small-scale farmers into modern agriculture by establishing a close interest connection mechanism. This paper, supported by the stakeholder theory and the theory of farmers’ behavior, adopted the single-case in-depth analysis method to study the Jinning Kunyang Zhangliang Flower Professional Cooperative in Yunnan Province. The high investment, high risk, technology-intensive, and strong market volatility of the flower industry contrasted with the limited rationality of small-scale farmers who “avoid risks and pursue stable income”. The Kunyang Zhangliang Flower Professional Cooperative has effectively addressed the problem of “loose connection and insufficient income” in farmers’ professional cooperatives through three endogenous paths: market-oriented operation of “land rental + farmers’ cash shareholding”, technology empowerment in flower planting and management, and the “land rent + share dividend” interest-sharing mechanism. It has formed a multi-level and institutionalized mechanism with farmers, including “income guarantee + brand premium + full-process technical management + equity dividend + village-enterprise collaboration”, transforming small-scale farmers from “marginal participants” to “core stakeholders”. Finally, based on national policy arrangements, targeted suggestions are put forward to provide references for similar specialized agricultural cooperatives in building a close interest connection mechanism.