Nitrate isomerization and reduction to ammonium（DNRA）is conducive to nitrogen fixation in the soil. The effects of long-term different nitrogen application on microbial abundance and community structure of DNRA process in paddy soil were studied to provide scientific basis for rational fertilization in paddy fields. Four treatments of no nitrogen fertilizer（CK）， conventional urea（NPK），controlled-release urea（CRU1）and controlled-release urea with 30%nitrogen reduction（CRU2） were set up，and the abundance and community structure of DNRA bacteria in rice soil were analyzed by fluorescence quantitative PCR and high-throughput sequencing. The results showed that nitrogen fertilization had a certain inhibitory effect on DNRA bacteria，the nrfA gene abundance showed as CK＞CRU2＞CRU1＞NPK，and NPK treatment was significantly different from CK（P＜0.05）. The dominant phylum of DNRA bacteria in rice soil were Proteobacteria，Verrucomicrobia and Planctomycetes and so on. The relative abundance of Planctomycetes was increased under nitrogen fertilization，while the relative abundance of Proteobacteria was decreased. The relative abundance of Proteobacteria in CRU1 treatment was the lowest but that of Planctomycetes was the highest. RDA analysis showed that Proteobacteria was positively correlated with soil pH and total sulfur，negatively correlated with organic matter，total nitrogen，nitrate nitrogen and ammonium nitrogen，and Planctomycetes was positively correlated with organic matter，total nitrogen and hydrolyzable nitrogen，negatively correlated with soil pH，total sulfur and ferrous iron. The Shannon and Simpson diversity indices were the highest in CRU1 treatment. Therefore，the application of controlled-release nitrogen fertilizer improved the microbial community and structure of the DNRA process in paddy soil，which was beneficial to the nitrogen retention in the field ecosystem.