The digital economy, as a new economic form with high information density, provides a new driving force for the realization of high-quality agricultural development. Panel data of 31 provinces in China from 2011 to 2020 were selected for analysis. The static panel data interaction effect model and panel threshold model were used to verify the nonlinear influence mechanism and heterogeneity of financial development in the process of the digital economy affecting high-quality agricultural development. The findings are as follows. (1) During the study period, the high-quality development of China’s agriculture showed a steady upward trend; however, the regional differences were significant, and the eastern part was larger than the central and western part. (2) The digital economy can promote high-quality agricultural development. (3) The digital economy has a double threshold effect in the process of affecting high-quality agricultural development, which depends on the level of financial development. When the threshold is exceeded, the digital economy has a more significant promoting effect on high-quality agricultural development. (4) The impact of the digital economy on high-quality agricultural development is heterogeneous. From the perspective of different regions, the impact effect is greatest in the eastern region, while the effect is smaller in the central and western regions. From different resource endowments, the positive impact effect is greatest in the major grain-selling areas, followed by the major grain producing areas, but the positive digital economy driving effect is not significant in the balance of production and sales areas. Finally, three policy suggestions are proposed. First, the Chinese government should increase investments in and support for digital technology to promote the integration of the digital economy and agriculture. Second, the Chinese government should promote the development of digital inclusive finance in areas with financial development below the threshold. Third, different regions should implement differentiated digital economies to promote high-quality agricultural development.