Abstract: Controlling cropland non-point source pollution plays an important role in the battle of agricultural and rural pollution prevention and control in China. Strengthening cropland non-point source pollution control is conducive to promoting the transformation of agricultural development mode, and achieving the sustainable utilization of cultivated land resources. Farmers are the main body of micro decision-making in agricultural production, whose willingness to accept is the key to their effective participation in cropland non-point source pollution control. Based on 353 questionnaires of farmers in the Dongting Lake Basin, this paper analyzed the mechanism of action among farmer differentiation, ecological cognition, and farmers’ willingness to accept for cropland non-point source pollution control with the PLS-SEM method. The research shows that: (1) Farmer differentiation has a significant positive impact on the willingness to accept. Besides, the farmers with a high degree of differentiation have a higher willingness to accept; (2) Ecological cognition plays a mediating role in the process of the impact of farmer differentiation on the willingness to accept for cropland non-point source pollution control. Farmer differentiation can positively affect farmers′ ecological cognition, and then enhance farmers′ willingness to accept for cropland non-point source pollution control; (3) Farmers’ age and labor ratio have a significant impact on their willingness to pay for participating cropland non-point source pollution control. Therefore, it is necessary to understand the interests of farmers, formulate reasonable compensation policies for cropland non-point source pollution control and improve farmers’ ecological cognition for arising farmers’ enthusiasm for participating in cropland non-point source pollution control.