The development of the digital economy aligns with the demands of high-quality growth and is a crucial means of achieving carbon neutrality goals. This study empirically analyzes the effects and mechanisms of the digital economy on agricultural carbon emissions using data from 31 provinces in China from 2011 to 2021. The results indicate that: (1) There exists an inverted U-shaped relationship between the digital economy and agricultural carbon emissions, with a positive slope at the minimum value of the digital economy and a negative slope at the maximum value. (2) Heterogeneity analysis shows a notable inverted U-shaped relationship in the northern regions, key grain-producing areas, and areas where production and consumption are balanced. (3) Rural industry integration partially mediates the inverted U-shaped relationship between the digital economy and agricultural carbon emissions, indirectly influencing agricultural carbon emissions. (4) The impact of the digital economy on agricultural carbon emissions is influenced by innovations in agricultural technology. Thus, it is recommended to enhance regional collaboration in the digital economy, harness digital technologies, and advance the seamless integration of digital and agricultural sectors to achieve modernization and high-quality growth in agriculture.