Abstract: The benefit linkage between farmers and cooperatives plays an important role in promoting organized agricultural production and increasing farmers’ income. Based on survey data collected from farm households in five counties of Sichuan Province, this study employs a Multinomial Endogenous Switching Regression model to examine the impact of transaction characteristics on farmer–cooperative benefit linkage models and to analyze how different linkage models affect farmers’ income. The results show that: first, transaction characteristics significantly influence the choice of benefit linkage models. Asset specificity such as investment in agricultural machinery and production facilities, as well as uncertainty in agricultural production, significantly promote farmers’ participation in horizontal cooperation, vertical collaboration, and vertical integration with cooperatives. Second, all three types of benefit linkage models significantly increase farmers’ income, and the results remain robust after a series of robustness tests. Third, heterogeneity analysis indicates that the income-increasing effect is stronger for farmers with larger planting scales. Vertical collaboration and vertical integration generate stronger income effects in areas with a higher density of cooperatives, whereas horizontal cooperation has a more significant income effect in areas with a lower density of cooperatives. In terms of income structure, horizontal cooperation significantly increases non-agricultural income, vertical collaboration significantly increases agricultural income, and vertical integration significantly increases both agricultural and non-agricultural income. Fourth, horizontal cooperation raises non-agricultural income by promoting farmland transfer and non-agricultural employment; vertical collaboration increases agricultural income by encouraging green production; and vertical integration improves both agricultural and non-agricultural income through the combined effects of these mechanisms. Based on these findings, this study suggests strengthening the foundation of farmer–cooperative benefit linkages, promoting precise matching between service supply and farmers’ demand, and improving the systems of land transfer, employment services, and green certification to broaden farmers’ income channels.