The process of urbanization leads to the reallocation and adjustment of agricultural production factors, which has a significant impact on agricultural carbon emissions (ACEs). Based on the panel data of 30 provinces in China from 2007 to 2019, this study explores the mechanism of how urbanization affects ACEs and conducts empirical tests. The results show that there is an “inverted U-shaped” relationship between urbanization and ACEs, with ACEs first increasing and then decreasing as the urbanization rate increases. From the perspective of intermediate mechanisms, urbanization mainly influences ACEs through the scale of farmland operations, the structure of crops, and the intensity of agricultural mechanization. Agricultural land management scale and crop structure have an inhibitory effect on ACEs, but the increasing intensity of agricultural mechanization exacerbates ACEs. In terms of regional heterogeneity, due to differences in physical geography and agricultural policies, the impact of urbanization on ACEs occurs in northern areas and non-major grainproducing areas. The spatial analysis indicates that urbanization has a spatial spillover effect on ACEs in the neighboring provinces. This study contributes to the existing ACEs’ literature by integrating urbanization, agricultural land use, and ACEs into the same theoretical analytical framework, exploring the underlying mechanisms, spillover effects, and regional heterogeneity.