Relationship between soil aeration, soil fertility and bacterial community structure was less known so far, particularly under the oxygen and nitrogen coupled irrigation. In this study, a three-factor randomized block experiment was designed with two levels of nitrogen application rate as 225 and 300 kg/hm2, two aeration levels of air void fraction as 15% and 0, and two levels of irrigation amount of 0.6 and 0.9 times of crop/pan coefficient on the experimental farm of North China University of Water Resources and Electric Power (34°47′5.91″N, 113°47′20.15″E), Henan province, China. Taking the greenhouse pepper as test crop, a high-throughput 16S genome sequencing technique was used to investigate the effects of oxyfertigation on soil aeration, soil chemical index, and soil bacterial community in the rhizosphere. The results showed that the oxyfertigation improved significantly the soil aeration, fertility, rhizosphere soil bacterial diversity, and community structure. Compared with non-aeration treatment, the soil dissolve oxygen, soil respiration, and soil redox potential in the treatments of 300 kg/hm2, 15% air void fraction, 0.6 and 0.9 times of crop/pan coefficient increased by 16.73%, 38.78%, 26.04% and 18.58%, 46.58%, 29.09%, respectively on the 3th day after irrigation at fruit expanding period (P<0.05). Compared with the non-aeration treatments, the average soil dissolve organic carbon, nitrate content increased by 26.40%, 28.22% under the treatments of 225 kg/hm2 nitrogen rate, 15% air void fraction, 0.6 times of crop/pan coefficient, while increased by 19.67%, 18.46% under 225 kg/ hm2 nitrogen rate, 15% air void fraction, 0.9 times of crop/pan coefficient (P<0.05), respectively. Compared with the non-aeration treatments (P<0.05), the average soil dissolved organic carbon, nitrate increased by 20.38%, 19.25% in the treatments of 300 kg/ hm2 nitrogen rate, 15% air void fraction, 0.6 times of crop/pan coefficient, and increased by 17.49%, 17.93% in 300 kg/ hm2 2 nitrogen rate, 15% air void fraction, 0.9 times of crop/pan coefficient, respectively. In nitrogen metabolism, the rhizosphere aeration and high nitrogen application can promote the content of Nitrospira associated with nitrification, and Bacillus associated with nitrogen fixation, while inhibit Pedomicrobium associated with denitrifying bacteria under soil aeration. The Shannon and Pielou-e index significantly increased in the aerated treatment, compared with the non-aeration treatment (P<0.05). Furthermore, the Pielou-e index significantly increased in the treatment of high irrigation and normal nitrogen rate (P<0.05), compared with low irrigation and low nitrogen treatments. In the phylum and class level, the copies of Proteobacteria, Actinobacteria, Acidobacteria, Alphaproteobacteria, and Deltaproteobacteria increased (P<0.05), whereas, the abundance of Gammaproteobacteria decreased, in the aerated treatments, compared with the non-aeration treatments (P<0.05). The copies of Proteobacteria decreased significantly (P<0.05), whereas, the abundance of Acidobacteria increased (P<0.05), in the high irrigation treatments, compared with the low irrigation treatment. The abundance of Proteobacteria and Alphaproteobacteria increased under a high nitrogen rate, compared with low nitrogen rate (P<0.05). Correlation analysis showed that the improvement of soil aeration significantly increased the diversity and uniformity of soil bacteria community in the rhizosphere, and the relative abundance of Acidobacteria at the level of phylum, thus to enhance the soil fertility for soil health, while suppress diseases in the soil rhizosphere environment. Therefore, results of this research would provide a theoretical basis for efficient utilization of water and fertilizer in the greenhouse pepper cropping system.