Agricultural carbon mitigation is one of the most important components of China’s carbon mitigation goals. This paper calculates China’s agricultural carbon emissions (ACEs) from 2000 to 2020, studies the spatio-temporal evolution characteristics of China’s ACEs, and aims to provide references for the development of China’s ACEs reduction policies. The results show that the total ACEs in China presented an inverted “W” trend, with a slight increase of 2.81% in total. China’s ACEs mainly came from livestock and poultry breeding and agricultural material inputs. Although the carbon emissions from rice cultivation and soil accounted for a relatively low proportion, they showed an uptrend of fluctuation during the study period. From a geographical point of view, ACEs in the regions of central China and western China were relatively high compared to those in eastern China. Carbon emissions decreased for crop farming and livestock and poultry breeding in most eastern provinces. Crop farming carbon emissions grew, while the emissions from livestock and poultry breeding declined in most of the central provinces. Carbon emissions increased for crop farming and livestock and poultry breeding in most western provinces. Therefore, the existing low-carbon agricultural policies should be optimized, crop farming technologies should be improved, and specific policies should be applied in the corresponding regions to support China’s ACEs reduction.