The green development of FinTech empowerment has become a compelling theme in economic development. In this study, based on the weighted least squares (WLS) and threshold regression methods of cross-sectional data, we empirically examine the impact of FinTech development on agricultural nonpoint source (NPS) pollution, a major cause of impaired surface water quality. Our results show that there is an inverted “U” shape relationship between the development of FinTech and agricultural NPS pollution. That is, after crossing a “threshold value”, the level of FinTech development can curb agricultural NPS pollution. At the structural level, the availability of FinTech services, the FinTech infrastructure, and the agricultural NPS pollution also have an inverted “U” shape relationship. At the threshold effect, in the developing stage of an agricultural economy, the overall level of FinTech development, the use of FinTech services, the availability of FinTech services, and the FinTech infrastructure have an inverted “U” shape relationship with agricultural NPS pollution. On the other hand, in the developed stage of an agricultural economy, the impact of FinTech development and its structure on agricultural NPS pollution is insignificant. Hence, we can conclude that FinTech development can help reduce agricultural NPS pollution in under-developed regions. However, due to the fact that a “U” shape relationship always exists between FinTech service quality and agricultural NPS pollution, the quality of FinTech service should be the main focus to reduce agricultural NPS pollution more effectively.