Constructing a long-term and stable interest linkage mechanism is an inevitable trend in the realization of agricultural industrialization and an important way to increase farmers’ income. Taking family farms in Hunan Province as the research object, this paper constructed an evaluation index system for the effectiveness of the benefit linkage mechanism from three dimensions of institutional benefit, governance level, and growth ability to analyze the effectiveness of the linkage mechanism between family farms and agricultural enterprises and compared different results by the entropy TOPSIS model and the obstacle factor diagnosis model. Results show that the organization modes of family farms and agricultural enterprise benefit linkage mechanism are mainly divided into three categories: shareholding, contract, and buyout. The comprehensive effectiveness scores in descending order are shareholding, contract, and buyout. From the perspectives of the weight of the standard level and the governance level, the system benefit weight is relatively large, and the weight of the growth ability is general. From three dimensions of the evaluation index system, although the shareholding type score is higher than those of the contract type and the buyout type, the three model scores are generally low with much room to improve. The growth rate of operating income, default costs, risk capital, the number of involved households, the proportion of secondary income, and the amount of guarantee are the main factors that affect the effectiveness of contractual and shareholding mechanisms. Therefore, this paper suggests that the relevant government departments should focus on promoting the development of the share-based benefit linkage model when strengthening the benefit linkage mechanism between family farms and agricultural enterprises, improve the ability of family farms to grow, innovate risk sharing and benefit distribution mechanisms, and enhance the profitability of partners.