Abstract: The in-depth study of the spatial and temporal development characteristics of the synergy between agricultural pollution reduction and carbon emission reduction in China and its driving factors is an experience and also a reference for resolving the inconsistency in agricultural environmental policy formulation, improving the effectiveness of policy implementation, and promoting the synergy and efficient governance of agricultural pollution reduction and carbon emission reduction. Based on the agricultural production data of 31 provinces in China from 2001 to 2021, this paper measures agricultural carbon emissions and surface source pollution in each region, and adopts the coupled coordination model to assess the synergy between agricultural carbon emissions and surface source pollution in each region of China, and on this basis, analyses the spatio-temporal development characteristics of China′s agricultural carbon emissions, surface source pollution, and the synergy between the two; and then adopts the GTWR model to further explore the synergy and its driving factors from the industry, elemental and environmental levels. Then, the GTWR model was used to further explore the driving factors of the synergistic effect of agricultural pollution reduction and carbon reduction in China at the industrial, elemental and environmental levels. The results show that: From 2001 to 2021, China′s agricultural carbon emissions showed a trend of slow growth followed by slow decline, agricultural surface pollution generally showed a fluctuating upward trend, agricultural carbon emissions and surface pollution are mainly concentrated in the major producing provinces and the major grain-producing areas; From 2001 to 2021, China′s synergistic effect of agricultural pollution reduction and carbon reduction showed an increasing trend of development, and there is obvious spatial heterogeneity in different regions; agricultural production conditions, large-scale operation, and the degree of synergistic effect of agricultural pollution reduction and carbon reduction in China have a significant spatial heterogeneity. Agricultural production conditions, the degree of large-scale operation and the level of agricultural agglomeration are the main driving factors for the synergistic effect of agricultural pollution reduction and carbon reduction, and there is significant spatial heterogeneity in the driving effect of each factor. It is recommended that each region should establish a sound system and control mechanism for the synergistic prevention and control of agricultural carbon emissions and surface pollution, build a cross-regional synergistic system for agricultural carbon emissions and surface pollution that is common, shared and win-win, improve agricultural production conditions, promote large-scale agricultural operations and increase the level of agricultural agglomeration, so as to promote the synergistic and efficient management of China′s agriculture to reduce pollution and reduce carbon emissions.