This study evaluates the impact of green finance on agricultural non-point source pollution control and emission reduction in 30 Chinese provinces from 2005 to 2022. Utilizing the entropy value method and the unit survey inventory method, the research measures the levels of green finance development and agricultural non-point source pollution. It employs a mediation effect model to empirically assess the pollution control efficacy of green finance and to elucidate the mechanisms underlying its influence. The findings indicate that green finance development significantly curtails agricultural non-point source pollution emissions. This conclusion is still valid after a series of robustness tests. The results of mechanism analysis show that environmental regulation and land transfer are important channels for green finance to reduce agricultural non-point source pollution. However, the slowing effect of green finance is stronger in provinces where the economic development level is still in the catch-up zone. Consequently, this study suggests strengthening green finance infrastructure in rural areas, coordinating green finance and environmental regulation policies, optimizing land transfer systems to promote scale management, and developing differentiated green finance policies based on regional economic development levels. These measures aim to augment the role of green finance in pollution treatment and emission reduction, thereby optimizing the green financial system, advancing environmental protection, and fostering sustainable development in China’s agricultural sector.