Carbon control involves more than just reducing carbon dioxide (CO2). Since the industrial revolution, approximately 35% of greenhouse gas (GHG) radiation has been from non-CO2 emissions. In this study, an Intergovernmental Panel on Climate Change coefficient method was used to calculate the agricultural non-CO2 GHG emissions in the farming -pastoral ecotone of Northern China. The study clarified the spatial and temporal evolution of non-CO2 GHG emissions in crop systems and livestock systems. The results showed that the total agricultural non-CO2 GHG emissions in the northern farming -pastoral ecotone from 2001 to 2021 were between 211.55x 104 t and 307.02 x 104 t, but the increase in the last decade was lower than that in the previous decade. Livestock and crop systems showed a trend of low emissions in the central region and high emissions in the northeast and southwest. The contribution of methane (CH4) to agricultural GHG emissions was greater than that of nitrous oxide (N2O), and the ratio of non-CO2 GHGs produced by livestock and crop systems was approximately 3:1. In livestock systems, the highest proportion of CH4 was produced by intestinal fermentation, accounting for 80%. In crop systems, N2O emissions from planting corn and the leaching of fertilizer and nitrogen contributed the most, accounting for 30%, 23% and 24%, respectively. The provinces of Shaanxi and Ningxia urgently need to find the cause of emissions and act to curb their further growth.