To clarify the impact mechanism of the digital economy on agricultural green total factor productivity, this paper conducts empirical tests based on provincial panel data from China spanning 2011 to 2023. The results indicate that the digital economy significantly enhances agricultural green total factor productivity. Furthermore, mechanism tests reveal that the digital economy improves agricultural green total factor productivity by strengthening local governments’ environmental concerns. Heterogeneity analysis shows that the eastern region, first-tier cities, and major grain-producing areas benefit more from the development of the digital economy, leading to greater improvements in agricultural green total factor productivity. Finally, threshold and spatial models unveil that the digital economy exhibits nonlinear characteristics of increasing “marginal effects” and spatial spillover effects. Accordingly, the paper proposes implementing differentiated digital empowerment strategies to fully unleash its spatial contributions to agricultural green development, providing policy references for fostering new quality productive forces in agriculture and promoting comprehensive rural revitalization.