Abstract: Replacing chemical fertilizer with organic fertilizer is an effective measure to deal with the problem of agricultural non-point source pollution. Improving farmers’ willingness to apply organic fertilizer is a prerequisite to promote the promotion of organic fertilizer. Based on the perspective of farmers’ differentiation and the theory of planned behavior, this paper innovatively uses the fuzzy set qualitative comparative analysis method and the survey data of 414 farmers in Zhejiang Province to conduct a configuration analysis of multiple concurrent causal relationships on the formation path of organic fertilizer application willingness of smallholder farmers and large-scale farmers. Seven formation paths of farmers’ willingness to apply organic fertilizer were obtained. Among them, the formation paths of smallholder farmers’ willingness to apply organic fertilizer can be divided into four types: learning type, external standard type, resource-oriented type and interest-oriented type. The formation paths of large-scale farmers’ willingness to apply organic fertilizer can be divided into three types: interest-oriented type, benefit oriented type and comprehensive type, indicating that there are behavior differences between the two types of agricultural business entities. Farmers’ willingness to apply organic fertilizer is the result of multiple factors. Targeted measures should be taken based on the production and management characteristics of farmers in different paths to improve the promotion efficiency of organic fertilizer and build a collaborative governance model of agricultural non-point source pollution with the participation of multiple subjects.