Water-saving irrigation strategies can successfully alleviate methane emissions from rice fields, but significantly stimulate nitrous oxide (N2O) 2 O) emissions because of variations in soil oxygen level and redox potential. However, the relationship linking soil N2O 2 O emissions to nitrogen functional genes during various fertilization treatments in water-saving paddy fields has rarely been investigated. Furthermore, the mitigation potential of organic fertilizer substitution on N2O 2 O emissions and the microbial mechanism in rice fields must be further elucidated. Our study examined how soil N2O 2 O emissions were affected by related functional microorganisms (ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), nirS, , nirK and nosZ) ) to various fertilization treatments in a rice field in southeast China over two years. In this study, three fertilization regimes were applied to rice cultivation: a no nitrogen (N) (Control), an inorganic N (Ni), i ), and an inorganic N with partial N substitution with organic manure (Ni+No). i +N o ). Over two rice-growing seasons, cumulative N2O 2 O emissions averaged 0.47, 4.62 and 4.08 kg ha-1 -1 for the Control, Ni i and Ni+No i +N o treatments, respectively. In comparison to the Ni i treatment, the Ni+No i +N o fertilization regime considerably reduced soil N2O 2 O emissions by 11.6% while maintaining rice yield, with a lower N2O 2 O emission factor (EF) from fertilizer N of 0.95%. Nitrogen fertilization considerably raised the AOB, nirS, , nirK and nosZ gene abundances, in comparison to the Control treatment. Moreover, the substitution of organic manure for inorganic N fertilizer significantly decreased AOB and nirS gene abundances and increased nosZ gene abundance. The AOB responded to N fertilization more sensitively than the AOA. Total N2O 2 O emissions significantly correlated positively with AOB and nirS gene abundances while having a negative correlation with nosZ gene abundance and the nosZ/nirS / nirS ratio across N-fertilized plots. In summary, we conclude that organic manure substitution for inorganic N fertilizer decreased soil N2O 2 O emissions primarily by changing the soil NO3--N, 3 --N, pH and DOC levels, thus inhibiting the activities of ammonia oxidation in nitrification and nitrite reduction in denitrification, and strengthening N2O 2 O reduction in denitrification from water-saving rice paddies.