Characterizing greenhouse gas (GHG) emissions and global warming potential (GWP) has become a key step in the estimation of atmospheric GHG concentrations and their potential mitigation by cropland management. However, the impacts of organic amendments on GHG, GWP, and yield-scaled GWP on cropland have not been well documented. Here, we investigate four amendment treatments (no amendment, mineral fertilizers, and pig slurry or crop residue combined with mineral fertilizers) during a two-year field experiment in rain-fed wheat-maize cropping systems. The results show that the average annual cumulative methane (CH4) flux ranged from −2.60 to −2.97 kg·C·ha−1 while nitrous oxide (N2O) flux ranged from 0.44 to 4.58 kg·N·ha−1 across all four treatments. N2O emissions were significantly correlated with soil inorganic nitrogen (i.e., NH4+-N and NO3−-N), and soil dissolved organic carbon (DOC) during both the winter wheat and summer maize seasons. On average, organic amendments combined with mineral fertilizers increased the annual GWP by 26–74% and yield-scaled GWP by 19–71% compared to those under only mineral fertilizers application. This study indicates that the fertilization strategy for Eutric Regosols can shift from only mineral fertilizers to organic amendments combined with mineral fertilizers, which can help mitigate GHG emissions and GWP while maintaining crop yields.