Abstract: Agricultural non-point source pollution and carbon emissions are significant environmental challenges in China’s agriculture sector. Existing studies have overlooked the synergistic relationship between controlling agricultural non-point source pollution and reducing agricultural carbon emissions. They have 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 aims to empirically examine the synergistic effect of reducing agricultural pollution and carbon emissions using panel data collected from 30 provinces in China from 2007 to 2021. The study utilizes a dual-fixed effect regression model and regulatory effect model to analyze the influencing mechanism of this synergistic effect. Additionally, the study explores the regional heterogeneity of this phenomenon. The results show that: 1) There is a synergistic effect on agricultural pollution reduction and carbon reduction, and there is a significant synergistic relationship between agricultural non-point source pollution and agricultural carbon emissions. 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 and agricultural investment scale have a significant negative regulation effect on the synergistic effect of agricultural pollution reduction and carbon reduction, the use efficiency of agricultural chemical materials has a significant positive regulation effect, and the agricultural planting structure has a positive regulation effect but not significant; 3)The northern agricultural pollution reduction carbon synergistic effect more significant than the southern region, agricultural chemical materials consumption structure and agricultural investment scale 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) It is imperative to uphold the grain production threshold and foster the development of large-scale and environmentally sustainable grain production. 3) It is imperative to increase investment in the agricultural sector and provide guidance for the modernization of agricultural practices. (4) Implement differentiated agricultural development strategies. Compared with other studies, the marginal contributions of this paper are as follows: 1) It proposed the concept of synergistic effect of agricultural pollution reduction and carbon reduction, analyzed specific synergistic effect of agricultural pollution reduction and carbon reduction, and discussed the possibility of synergistic solution between agricultural non-point source pollution and agricultural carbon emission; 2) The influence mechanism of the synergistic effect of agricultural pollution reduction and carbon reduction was further discussed. 3) The synergistic effects of agricultural pollution reduction and carbon reduction in different regions and their influencing mechanisms were analyzed.