<p>Agricultural waste is crucial for modern agricultural development, food security, ecological system development, and even agricultural carbon sinks. The theory of planned behavior (TPB) was used to provide a study framework for analyzing the mechanism of farmers’ adoption of organic fertilizers. First, a Probit model was used to investigate the determinants influencing farmers’ adaptation to organic fertilizers in Qionglai, Sichuan province, in southwest China. Second, the instrumental variable method was used to check the endogeneity of the Probit model. Finally, the stepwise regression method was utilized to investigate the mediating mechanism of farmers’ adoption of organic fertilizers. The following are the main findings: (1) Without considering the model’s endogeneity, risk perception, farmers’ health, the location of farmed land, and soil fertility all substantially impact paddy farmers’ use of organic fertilizers. (2) When endogeneity is taken into account, risk perception is the most critical factor influencing farmers’ adoption behavior of organic fertilizer, and the intention to accept machinery organic fertilizer application is an endogenous explanatory variable with a 44.41% degree of influence between farmers’ knowledge of organic fertilizer availability and organic fertilizer application. This suggests that the perceived availability of organic fertilizers directly affects adoption behavior. However, the intention to adopt the application machinery for organic fertilizers supplied by cooperatives plays a notable mediating role. Enhancing farmers’ understanding of organic fertilizer availability and bolstering their willingness to embrace the corresponding machinery simultaneously could significantly elevate the prevalence of organic fertilizer adoption behavior.</p>