As a traditional agricultural powerhouse, China's agricultural development model characterized by high consumption, high input, and high demand continues to drive the continuous increase in China's total non-CO₂ greenhouse gas emissions from agriculture. Non-CO₂ gases from agricultural sources, predominantly CH₄ and N₂O with high warming potential, are the main contributors. Controlling non-CO₂ greenhouse gas emissions from agricultural sources is a crucial aspect for China to achieve agricultural green development and its "dual-carbon" goals. The accounting of non-CO₂ greenhouse gases in China's agricultural system is still in a process of continuous exploration and improvement, with no complete and universally recognized system established yet in terms of estimation methods and model parameters. This study, referencing the IPCC classification method, established an accounting system for non-CO₂ greenhouse gas emissions from agriculture tailored to the characteristics of China's agricultural system, including crop cultivation, animal husbandry, and agricultural waste, and conducted an assessment of China's agricultural greenhouse gas emissions in 2020 as the baseline. The results showed that the total non-CO₂ greenhouse gas emissions from China's agricultural system amounted to 62801.68 ten thousand tons of CO₂-e, with CH₄ being the largest contributor, accounting for 71% of the total emissions. In terms of individual emission categories, emissions from livestock farming reached 33,205.34 ten thousand tons of CO₂-e, exceeding 50% of the total emissions, followed by emissions from crop production at 28,617.93 ten thousand tons of CO₂-e; agricultural waste emissions were relatively low, at only 978.42 ten thousand tons of CO₂-e.The types of greenhouse gas emissions from China's agricultural system exhibited obvious spatial differentiation characteristics; emissions from livestock farming dominated in the northwest, north China, and southwest, while emissions from crop production dominated in east China and south China. The northeast and central China regions were relatively special, with a mixture of emissions from livestock farming and crop production, as well as dual dominance of emissions from crop cultivation and animal husbandry. Agricultural waste emissions were mainly concentrated in the northeast and east China regions, where crop production was relatively developed. The greenhouse gas accounting constructed in this study fully reflects the current status of China's agricultural greenhouse gas emissions and the emission structure of agricultural greenhouse gases in each province, which is conducive to the formulation of targeted agricultural planning policies in various regions. It also provides methodological support and data basis for reducing uncertainties in Chinese agricultural greenhouse gas accounting research and clarifying the contribution of the agricultural system to carbon neutrality.