Abstract: As an environmentally friendly means of agricultural production, applying organic fertilizer can improve the current situation of agricultural environmental pollution. In order to explore the reasons for the paradox existing between farmers’ pro-environmental behavior and willingness, taking the application of organic fertilizer as an example, based on the data of farmers’ field investigation, this paper uses binary Logistic model to analyze the reasons behind the inconsistency between the behavior and willingness of farmers in the process of applying organic fertilizer from the perspective of cognitive characteristics, psychological characteristics and external situational factors. The results show that there is a paradox existing between farmers’ organic fertilizer application behavior and willingness, and farmers’ understanding degree on organic fertilizer, perceptual behavior control, social responsibility, social norms, the body situation, educational level, family income, the block number of land and the income of organic fertilizer are the causes of this phenomenon. Besides, the results show that for some farmers whose educational level is higher, their cognitive level on agricultural pollution is higher and their cognitive level on agricultural pollution’s harm on their health is higher, the possibility of the existing of paradox between their organic fertilizer application behavior and willingness is lower. For some older farmers and female farmers, when their living place is further away from their land and their land’s transportation is worse, the possibility of the existing of paradox between their organic fertilizer application behavior and willingness is higher. According to these results, this paper suggests that we should improve the whole cognitive level of farmers whose educational level is higher, strengthen the propaganda of the application of organic fertilizer, make proper social norms about organic fertilizer’s application, increase subsidies for the application of organic fertilizers, adjust land under the situation that taking older farmers and women farmers into consideration, and then reduce the land’s fragmentation degree and other policy recommendations to promote the transformation of farmers’ organic fertilizer application willingness into behavior.