The impact of the rural digital economy on agricultural carbon emissions and green technological innovation is fragmented, while the influence of the digital economy and carbon emissions on urban and industrial areas has attracted the attention of many scholars. It is necessary to further investigate the relationship between the rural digital economy and its impact on agricultural carbon emissions and green technological innovation. This study explores the impact of agricultural green technological innovation on carbon emissions and its transmission mechanism. It examines the effects of rural digital economy on agricultural carbon emissions, as well as the intermediary effect of agricultural green technology innovation, using panel data from 30 provinces in China (excluding Xizang, Hong Kong, Macao and Taiwan) between 2012 and 2021. The results indicate that the rural digital economy has a significant impact on reducing agricultural carbon emissions. This effect remains robust even after conducting a series of rigorous tests, including substituting the dependent variable. Additionally, the influence of the rural digital economy on agricultural carbon emissions is particularly notable in the western and northeast regions, as well as in provinces with limited levels of rural digital economic growth. Furthermore, promoting innovation in green agricultural technology through the advancement of the digital economy in rural areas can lead to a reduction in carbon emissions from agriculture. The research findings suggest promoting distinctive growth in the rural digital economy, elevating the standard of eco-friendly technology innovation in agriculture, and advancing the eco-friendly and low-carbon progress of both the rural digital economy and agriculture.