Under the background of China's “double carbon” goal, digital economy has become an important way to reduce carbon emissions in China. This paper utilizes the provincial panel data of China from 2012 to 2022, introduces the perspective of agricultural science and technology innovation, empirically examines the impact mechanism of regional digital economy development on agricultural carbon emission through regression analysis model, and portrays the dynamic effect and spillover effect of digital economy development on agricultural carbon emission from both time and space dimensions. The empirical results show that: digital economic development will have a significant inhibitory effect on the intensity of agricultural carbon emissions, and the inhibitory effect will be indirectly affected through the path of agricultural scientific and technological innovation; the impact of digital economic development on the intensity of agricultural carbon emissions there is a time lag effect, the current stage of the digital economic development will still have a strong inhibitory effect on the intensity of agricultural carbon emissions in the future; Digital economic development has a spatial spillover effect, i.e., the development of the regional digital economy will have an inhibitory effect on the intensity of agricultural carbon emissions in neighboring provinces. Based on this, it is proposed to strengthen the construction of digital infrastructure, promote the coordinated development of the digital economy in the region, and formulate policies to reduce carbon emissions in agriculture.