This study investigates the mechanisms by which green finance mitigates non-point source pollution. Based on provincial panel data from China spanning 2005 to 2023, this study conducts an empirical analysis that yields several key findings: (1) The development of green finance significantly reduces the intensity of agricultural non-point source pollution. (2) Green finance indirectly contributes to pollution reduction by incentivizing farmers to adopt environmentally sustainable production practices. (3) The pollution control effects of green finance are amplified in regions with advanced digital infrastructure. (4) The impact of green finance on agricultural pollution demonstrates a threshold effect associated with regional innovation capacity—only when innovation capability exceeds a certain threshold does the emission reduction effect of green finance become evident. Theoretically, this study broadens the research dimensions of green finance by integrating farmer behavioral factors and revealing boundary conditions related to technology and innovation. Policy implications include the need to tailor green financial products for agriculture, accelerate the development of rural digital infrastructure, and implement innovation-driven differentiated policies to enhance precision.