In the perspective of new institutional economics, we regard farmers’ cooperatives as a “contractual set” integrating a series of long-term contractual relations, and transform the selection problem of organization forms into selection problem of contractual model within organization. By the theoretical framework of Transaction Cost Economics, we analyze the formation mechanism and determinant factors of contractual model of different farmers’ cooperatives and conduct case study on Production and Marketing Cooperative of Sweet Pomegranate in Mengzi, Yunnan. The results show that selecting contractual forms of cooperatives is the result of weighing many factors; new organization model or contractual arrangement is complementary to the former system arrangement; the selection of cooperatives model is an important factor impacting cooperation efficiency and stability of organization. One organization model with efficiency not only hinges on the transaction characteristic of organization, but also considers the compatibility with exterior transaction environment. In the process of selecting contractual model, we should conform to objective evolving law, but not be in thrall to a certain given form.