Abstract: Agricultural non-point source pollution and carbon emissions pose significant environmental challenges for China’s agricultural sector. Previous studies have overlooked the synergistic relationship between controlling agricultural non-point source pollution and reducing carbon emissions. They also failed to investigate the combined effect of reducing agricultural pollution and carbon emissions as well as the mechanisms that influence this effect. This oversight has had an impact on the sustainable development of agriculture. This study empirically examined the synergistic effect of reducing agricultural pollution and carbon emissions using panel data collected from 30 Chinese provinces from 2007 to 2021. This study utilized a dual-fixed effect regression model and regulatory effect model to analyze the influencing mechanism of this synergistic effect. In addition, this study explored the regional heterogeneity of this phenomenon. The results show that: 1) a synergistic effect on agricultural pollution reduction and carbon reduction and a significant synergistic relationship between agricultural nonpoint source pollution and agricultural carbon emissions exist. When agricultural non-point source pollution is reduced, agricultural carbon emissions will also be significantly reduced, and this result is still valid after robustness test and endogeneity treatment; 2) the consumption structure of agricultural chemical materials have a significant negative adjustment effect on the synergistic effect of agricultural pollution reduction and carbon reduction, the use efficiency of agricultural chemical materials has a significant positive adjustment effect on agricultural planting structure, and the agricultural investment scale has a negative adjustment effect but not significant; 3) the northern agricultural pollution reduction carbon synergistic effect is more significant than that of the southern region, agricultural chemical materials consumption structure and use efficiency of agricultural chemical materials of the northern agricultural pollution reduction carbon reduction synergistic effect produce significant negative regulation effect, agricultural planting structure has a significant positive regulating effect on the synergistic effect of agricultural pollution reduction, and carbon reduction in both northern and southern regions. Therefore, this paper presents several recommendations. 1) In the context of agricultural environmental pollution control, it is crucial to prioritize the issue of agricultural chemical materials and implement strategies to minimize their irrational usage. 2) Upholding the grain production threshold and fostering large-scale environmentally sustainable grain production is imperative. 3) Increasing investment in the agricultural sector and providing guidance for modernizing agricultural practices is imperative. 4) Implementing differentiated agricultural development strategies. Compared with other studies, the marginal contributions of this study are as follows: 1) it proposes the concept of the synergistic effect of agricultural pollution reduction and carbon reduction, analyzes the specific synergistic effect of agricultural pollution reduction and carbon reduction, and discusses the possibility of a synergistic solution between agricultural non-point source pollution and agricultural carbon emissions; 2) the mechanism of the synergistic effect of agricultural pollution reduction and carbon reduction is further discussed; 3) the synergistic effects of agricultural pollution and carbon reduction in different regions and their influencing mechanisms were analyzed.