Abstract: China’ s economy has entered a stage of high-quality development. While remarkable economic achievements have been made, mounting challenges related to resources and the environment have become increasingly prominent. As a critical ecological security barrier for the country, the Yellow River Basin is plagued by severe issues such as pollution and ecological degradation. In 2024, General Secretary XI Jinping, when presiding over the symposium on comprehensively promoting ecological protection and high-quality development of the Yellow River Basin, charted a clear course for advancing ecological and environmental governance in the region. Against this backdrop, boosting the development of agricultural total factor productivity (TFP) in the Yellow River Basin has emerged as a key priority. Based on panel data from 57 prefecture-level cities in the Yellow River Basin from 2014 to 2023, this study employed the Super-efficiency SBM-GML model to measure agricultural TFP, and utilized methods such as the two-way fixed effects model and mediation effect model to empirically examine the impact and underlying mechanisms of digital financial inclusion on agricultural TFP. The findings revealed the following: (1) In terms of the changing trend of agricultural TFP, the Yellow River Basin as a whole exhibited an inverted U-shaped pattern from 2015 to 2023. Regarding regional disparities, the differences in agricultural TFP among prefecture-level cities had narrowed year by year, with the overall level showing an upward trend. (2) Digital financial inclusion had significantly enhanced agricultural TFP. Specifically, both the depth of use and the degree of digitalization among its sub-indices contributed positively to agricultural TFP. (3) Mechanism tests indicated that financial agglomeration played a significant mediating role in the process through which digital financial inclusion influences agricultural TFP. (4) Heterogeneity analysis showed that the promoting effect of digital financial inclusion was more pronounced in the upper and lower reaches of the region, while it was not significant in the middle reaches. Accordingly, this study proposes policy recommendations such as implementing differentiated development strategies, strengthening financial agglomeration effects, and enhancing inter-regional digital infrastructure development.