Agriculture’s goal to meet the needs of the increasing world population while reducing the environmental impacts of nitrogen (N) fertilizer use without compromising output has proven to be a challenge. Manure and composts have displayed the potential to increase soil fertility. However, their potential effects on nitrous oxide (N₂O) and methane (CH₄) emissions have not been properly understood. Using field-scaled lysimeter experiments, we conducted a one-year study to investigate N₂O and CH₄ emissions, their combined global warming potential (GWP: N₂O + CH₄) and yield-scaled GWP in a wheat-maize system. One control and six different organic fertilizer treatments receiving different types but equal amounts of N fertilization were used: synthetic N fertilizer (NPK), 30% pig manure + 70% synthetic N fertilizer (PM30), 50% pig manure + 50% synthetic N fertilizer (PM50), 70% pig manure + 30% synthetic N fertilizer (PM70), 100% pig manure (PM100), 50% cow manure-crop residue compost + 50% synthetic N fertilizer (CMRC), and 50% pig manure-crop residue compost + 50% synthetic N fertilizer (PMRC). Seasonal cumulative N₂O emissions ranged from 0.39 kg N ha⁻¹ for the PMRC treatment to 0.93 kg N ha⁻¹ for the NPK treatment. Similar CH₄ uptakes were recorded across all treatments, with values ranging from −0.68 kg C ha⁻¹ for the PM50 treatment to −0.52 kg C ha⁻¹ for the PM30 treatment. Compared to the NPK treatment, all the organic-amended treatments significantly decreased N₂O emission by 32–58% and GWP by 30–61%. However, among the manure-amended treatments, only treatments that consisted of inorganic N with lower or equal proportions of organic manure N treatments were found to reduce N₂O emissions while maintaining crop yields at high levels. Moreover, of all the organic-amended treatments, PMRC had the lowest yield-scaled GWP, owing to its ability to significantly reduce N₂O emissions while maintaining high crop yields, highlighting it as the most suitable organic fertilization treatment in Sichuan basin wheat-maize systems.