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Air injection and irrigation affect soil aeration, oxygen partial pressure and nitrogen turnover, which are bound to affect the processes of nitrification and denitrification, and influence production and emission of N2O. In order to study the response of soil N2O fluxes to nitrifying and denitrifying bacteria under aerated irrigation, the experiment was conducted in greenhouse tomato fields from August to December, 2016. Based on the irrigation amount of adequate water supply (W), 0.6W, 0.8W and 1.0W were set as three different irrigation regimes. Each irrigation regime contained aeration and non-aeration. Hence, six treatments were set. The results showed that a downward trend of soil N2O fluxes was observed during the earlier stage of tomato, while soil N2O fluxes held at a relatively stable and low level since 25 d after transplanting. Compared with non-aerated irrigation, aerated irrigation increased soil N2O emissions by 4.7% on average. Soil N2O emissions were increased with the increase of irrigation volume, which were increased by 1.9% on average. But the treatment effects between aeration and irrigation regimes on soil N2O emissions were not significant （P＞0.05). In terms of the mean values of microbial population throughout the whole tomato growth period, nitrifying bacteria under aerated irrigation was increased by 2.1% on average compared with non-aerated irrigation, and denitrifying bacteria was decreased by 9.7% on average （P＞0.05). In addition, nitrifying and denitrifying bacteria were increased with the increase of irrigation amount （P＞0.05). Correlation analysis showed that the dependence of soil N2O flux on WFPS and soil temperature showed a significantly positive correlation under all treatments （P＜0.01). The soil N2O flux was significantly and negatively correlated with denitrifying bacteria under different irrigation modes （P＜0.01). The research results provided theoretical foundation for the process of nitrification and denitrification, and for the nitrogen cycle in the protected vegetable fields.