Accelerating the development on industry chain and value chain of the export-oriented agriculture is an effective way for farmers income growth, and the wish for the farmers to join cross-border Agri-food Supply Chains is comprehensively affected by the factors such as farmer household feature, production capacity, institution (policy) and so on. The empirical analysis based on southwest area farmer household questionnaire shows that such three aspects as farmer household feature (education degree, land area, family income), production capacity(production scale, business cost, commercialization level) and institution (supply chain alliance institution, governmental supervision and protection policy, governmental subsidy policy) have direct or indirect impact on the wish of farmers to participate in cross-border Agri-food supply chain, and that its impact degree in order is institution factor>production capacity>farmer household feature. Farmer households should be accelerated to be transformed into new-type vocational farmers, farm head and family farm, cross-border Agri-food supply chains and their core enterprises should protect the interests of the farmers, governments should perfect the institutional environment in order to strengthen the wish of the farmers to participate in cross-border Agri-food supply chains. 