Abstract: In order to strengthen the understanding of the internal logic of agricultural environmental policy from formulation to implementation, this article is based on the fairness perception and trust of farmers. This article constructed a theoretical framework for farmers’ to explain their agricultural environmental protection behavior under uncertainty. The data for farmers’ point of view was collected from Shanxi, Shandong and Shaanxi Province. The Path analysis, Bayesian nonlinear structural equation modelling, and Slope analysis methods were employed to test the hypothesis put forwarded in this article. The results showed that: (1) There were direct and indirect effects of farmers’ fairness perception on farmers’ behavior towards agricultural environmental policy. The impact of direct effect was much higher than the indirect effect. The direct effect indicated that the higher farmers’ perception of fairness was linked to highly motivate farmers to protect the agricultural environment. The indirect effect of farmers’ fairness perception showed that farmers’ fairness perception first enhanced the farmers’ trust, and then the trust in turn translated into the farmers’ agricultural environmental protection behavior. Likewise, (2) the uncertainty results of farmers’ agricultural environmental protection behavior had hindered farmers’ agricultural environmental protection behavior. Furthermore, the uncertainty results of farmers’ agricultural environmental protection behavior interfered with the transformation from farmers’ fairness perception to their behavior significantly. Based on the above results, it can be concluded that the farmers’ fairness perception and trust were important, and should be considered in agricultural environmental policy development. Therefore, previously used command-based agricultural environmental policies should be reconsidered. Similarly, the agricultural environmental policies which combined farmers’ participation should be implemented gradually as detecting the agricultural environment regularly and giving the feedback to farmers can be helpful to improve environmental conditions. Finally, this approach could not only reduce the uncertainty results of farmers’ agricultural environmental protection behavior and government regulatory costs but could also promote the effective implementation of agricultural environmental protection policies.