The reduction of substantial agricultural greenhouse gases (GHGs) emissions can make a significant contribution to climate change mitigation and regional sustainable development. Given that most of the current studies about eco-efficiency only considers CO₂, while ignoring other GHGs, such as CH₄ and N₂O, this study analyzes the spatiotemporal characteristics of CO₂, CH₄, and N₂O, and considers them as undesirable outputs to assess the agricultural eco-efficiency (AEE) in the North China Plain from 2004 to 2022, respectively, including AEECO₂, AEECH₄, AEEN₂O, and AEEGHG. The results show that (1) Agricultural GHGs emissions increased significantly before 2018 and slightly decreased after 2018, due to the enforcement of energy-saving and emission-reducing policies. Spatially, GHG emissions are higher in the north but lower in the south. (2) The study demonstrated that incorporating CH₄ and N₂O significantly affects efficiency (p < 0.01). AEECH₄ and AEEN₂O are higher than AEEGHG, while AEECO₂ is lower than AEEGHG, indicating that only considering a single emission will result in an inefficient outcome. (3) With significant regional heterogeneity, AEEGHG is higher in Henan, Beijing, and Tianjin, while it is the lowest in Hebei. Specific suggestions are proposed to promote sustainable agricultural development. This study presents a novel perspective for comprehensively assessing AEE and offers scientific evidences for agricultural policy formulation to promote climate mitigation.