Green manure is widely employed to substitute chemical N fertilizer. However, the potential of further alleviating N2O emission when combined with efficient management technologies has not been fully explored. To reduce this research gap, a 2-year field experiment was conducted in northwestern China. The aim was to investigate the impact of zeolite application on N2O emission in the maize-common vetch intercropping system under 30% N reduction, as well as the possible mechanisms. The experiment included two cropping systems, namely monoculture maize and maize-common vetch intercropping, along with three amendment practices, namely conventional N, 70% conventional N, and zeolite application under 70% conventional N. Compared with monoculture maize under conventional N, maize-green manure intercropping combined with zeolite application under 70% chemical N achieved comparable yields. Simultaneously, this practice reduced cumulative N2O and yield-scaled N2O emissions by 36.9% and 39.2%, respectively. This reduction can be attributed to a decrease in soil ammonium-N by 20.9%–57.7%, nitrate-N by 47.7%–51.3%, nitrate reductase activities by 25.3%–34.4% and N2O-producer (i.e., nirS and nirK) abundance by 17.3%–79.4% in denitrification, and an increase in the N2O-reducer (i.e., nosZ) abundance by 40.0%–103.4%. Compared with 100% N input, 70% chemical N treatment reduced ammonium-N by 22.3%–41.0%, nitrate-N by 25.4%–41.0%, and N2O-producer abundance by 17.1%–35.0% in denitrification. Zeolite application reduced denitrifying enzyme activities by 8.2%–12.9%, N2O-producer abundance by 42.5%–56.4%, but increased N2O-reducer abundance by 13.3%–23.3% in denitrification. PLS-PM analysis showed that N2O emission mitigation was mainly related to reduced soil ammonium-N and nitrate-N, decreased N2O-producer abundance, and increased N2O-reducer abundance in denitrification. These findings provide new insights into the fact that intercropping green manure combined with zeolite application effectively mitigates N2O emission by regulating mineral N, N-cycling enzymes, and denitrifier abundances while maintaining maize yield after cutting 30% N input.