Intensive irrigation coupled with excessive nitrogen (N) fertilizer input has resulted in high soil greenhouse gas (GHG) emissions in vegetable cropping systems. Biochar as a soil amendment has been advocated as a desirable option to reduce GHG emissions in agricultural systems, but its interactive effects with soil N availability in vegetable systems have yet to be clarified. We performed a field study to examine how biochar interacts with N fertilizer in driving annual methane (CH4) and nitrous oxide (N2O) emissions from an intensively-irrigated greenhouse vegetable cropping system acting as both sources of atmospheric CH4 and N2O in subtropical China. Biochar amendment significantly increased soil CH4 emissions by 33% and 85%, while it decreased soil N2O emissions by 22% and 12% with and without N fertilizer input, respectively. Fertilizer N combination weakened the positive response of CH4 to biochar while it enhanced the mitigation potential of biochar for N2O. Annual direct emission factors of fertilizer N for N2O were estimated to be 1.35% and 1.94% for the fields with and without biochar amendment, respectively. Annual flux-sustained global warming potential (SGWP) and greenhouse gas intensity (GHGI) were significantly decreased by biochar amendment, and this mitigation effect was enhanced with fertilizer N combination. Altogether, we highlight that biochar can reconcile higher yield and lower climatic impact in intensive vegetable cropping systems in subtropical China, particularly in vegetable soils with high N availability.