Human activities are one of the main reasons for increasing the concentration of greenhouse gases in the atmosphere and causing the natural greenhouse effect. Among them, agricultural production activity is one of the important sources of greenhouse gas emissions. Based on the emission factor method, this paper constructs a greenhouse gas emission accounting system of the agriculture including planting industry and livestock breeding industry. The study systematically calculated the total greenhouse gas emission trend of Chinese agricultural system from 1980 to 2020. More specifically, it calculated the greenhouse gas emission of Chinese agricultural system in 1980, 2000 and 2011 at the district and county level. Moreover, the temporal and spatial heterogeneity of greenhouse gas emissions in the agricultural systems at different stages was compared. It is found that the greenhouse gas emissions of the Chinese agricultural system showed a fluctuating growth trend from 1980 to 2020, with an increase of nearly 46%. CH₄, CO₂ and N₂O are the three major greenhouse gases emitted by the agricultural system. CH₄ is the greenhouse gas with the largest contribution to the emission of the agricultural system, which accounts for 47.33% of the total emission. The proportion of CO₂ in the greenhouse gas emissions from the agricultural system tends to increase. Changes in the share of N₂O in greenhouse gas emissions from agricultural systems are slight. From the perspective of the source of greenhouse gases in the agricultural systems, CH₄ emission mainly comes from rice field planting and crop straw combustion (56.20%). CO₂ emission mainly comes from the crop straw combustion (67.91%), and N₂O emission mainly comes from livestock breeding (50.89%) and nitrogen fertilizer application (31.05%). From the perspective of spatial distribution structure, greenhouse gas emissions from the Chinese agricultural system are related to agricultural production modes in different regions. The areas with high CH₄ emissions are mainly located in China's main rice-producing areas and dryland crop-producing areas. The areas with high CO₂ emissions are mainly located in the northeast, northwest and other regions and east China. The areas with high N₂O emissions are mainly located in the major livestock breeding areas in the northwest, and in the central and southern areas where the agricultural economy has a high level of development. This study helps to reveal the dynamic characteristics, current status, and spatial differences of China's agricultural greenhouse gas emissions, and provides a scientific reference for the realization of the dual-carbon goal from the perspective of agricultural emission reduction.