Agriculture is becoming a substantial contributor to carbon emissions in China, and the efficient reduction of agricultural carbon emissions (ACEs) has become a universal concern. Currently, the digital transformation of agriculture (DTA) provides a new way to reduce carbon emissions. However, questions regarding whether and how DTA suppresses ACEs remain the focus of both academic and practical attention; thus, they serve as the objectives of this study. Based on theoretical analyzes, the carbon emission reduction effect of DTA is empirically analyzed using panel data from 30 Chinese provinces between 2015 and 2021 with a benchmark regression model, mediating effect model and threshold effect model. The results show the following: (1) DTA significantly reduces ACEs. (2) DTA reduces ACEs through three paths: expanding the agricultural production scale, optimizing the agricultural industrial structure, and promoting agricultural technological progress. The agricultural industrial structure has the most considerable mediating effect, while the agricultural production scale expansion has the smallest effect. (3) The inhibitory effect of DTA on ACEs shows very distinct heterogeneity. DTA primarily reduces ACEs in eastern and nongrain production areas yet has an insignificant impact on other areas. In addition, the DTA has a significant inhibitory effect on ACEs from both fertilizers and diesel oil. (4) The inhibitory effect of DTA on ACEs is nonlinear rather than linear. There is a single threshold effect for the effect of DTA on ACEs, which is insignificant below the threshold and significantly negative above the threshold. Therefore, China’s central and local governments need to increase the level of DTA, encourage farmers to moderately expand the scale of their operations, emphasize the agricultural service industry, and enhance agricultural technological innovation to ultimately reduce ACEs.