Ferrous (Fe (II)) plays a key role in the production or consumption of N2O through biochemical pathways in paddy soil. Drying-wetting alternations can affect Fe cycling and the associated N2O emissions, however, the underlying microbial mechanisms remain largely unknown, particularly in plant systems with the presence of roots. In this study, a laboratory experiment with four Fe (II) levels (0, 50, 150, and 300 mg Fe (II) kg−1 dry soil) was conducted to investigate the response of N2O emission and denitrifying genes to iron (II) supplement in root zone and bulk region during wetting-drying cycles in paddy soils. The results indicated that supplemented Fe (II) led to a reduction in soil N2O emissions, predominantly observed during the drying phase. The bulk soil exhibited higher N2O fluxes compared to root zone. However, the decrease in cumulative N2O (cumul-N2O) by Fe (II) was significantly greater in bulk region than in root-affected soil (P < 0.001), registering 85–91 % reduction for soils amended with low to medium rates (50 and 150 mg Fe (II) kg−1 dry soil) throughout the experiment. This might be attributed to the more sensitive response of N2O reductase (nosZ gene) to low or medium Fe (II) supplementation in bulk soil than in root zone. The highest Fe (II) addition (300 mg Fe (II) kg−1 dry soil) showed a negative impact on nosZ-containing gene during initial flooding phase, resulting in the lower reduction rate (40 %) in cumulative N2O emission from bulk soil. Cross-correlation analysis showed that the changes of nosZ-containing genes in root zone occurred before variations of cumulative N2O data, indicating that compared to bulk soil, root zone soil exhibited a more pronounced of N2O consumption capability, especially after addition of ferrous. In summary, judicious Fe (II) application into soil promotes N2O reduction during wetting-drying alternation. The response of nosZ abundance to Fe (II) supplementation is likely the pivotal microbial factor influencing N2O emission reduction during wetting-drying alternation in paddy soil.