Abstract: With the acceleration of agricultural modernization, it has become an important topic to explore how small farmholders can realize the value-added of income by participating in the holistic agricultural industry chain. Based on the actual situation of small farmholders in Gansu Province, this paper constructed four attribute frameworks from the perspective of behavioral preference: farmer participation path, interest linkage mechanism, service supply and policy support. Based on the survey of 300 questionnaire data from 14 cities and prefectures, the participation preference and preference heterogeneity were empirically analyzed by using multiple Logit models. The results showed that: Firstly, small farmholders generally prefered to participate in the holistic agricultural industry chain through the “farmer cooperative” model, tended to choose stable linkage mechanisms such as order contracts, and had a strong demand for comprehensive services covering technical information, agricultural logistics and capital services, and policy-based financial support had become their preferred policy tool. Secondly, factors such as gender, age, education level, and income level significantly affected the choice of participation methods, showing strong individual heterogeneity. Thirdly, in terms of value-added income, cooperative participation, order contracts, financial support and comprehensive services had significantly increased the income level, while the participation of leading enterprises had a negative impact on the income appreciation of rural households. The results of this study provided a theoretical and practical basis for improving the policy design of the whole agricultural industry chain, improving the organizational level of small farmholders, and promoting the construction of modern agricultural system.