Diazotrophs can help minimize the use of synthetic nitrogen fertilizers by fixing atmospheric dinitrogen in agricultural ecosystems. However, the diazotroph community affected by biochar application is still poorly explored in the paddy fields. Here, a field study with three different biochar application rates, namely control (CK, no biochar amendment), low (LB, 24 t ha−1 applied once), and high (HB, 48 t ha−1 applied once), was employed in a double rice paddy. The impacts of biochar on diazotrophic abundance/community composition, soil chemical and biological properties, and rice biomass were examined 3‒4 years after application. The abundance and community composition of diazotrophs were measured with quantitative polymerase chain reaction and amplicon sequencing, respectively. Biochar application significantly enhanced the diazotrophic abundance by 13.1–94.2% compared with CK, which might result from increased stubble and root biomass, soil Olsen-P, total P, and total organic C. Compared to HB, LB significantly increased diazotrophic abundance by 5.6–20.8% three years post-addition, which was probably due to the increased stubble and root biomass. The variations in the alpha diversity index in diazotroph community composition from biochar treatments was decreased over time, relative to CK. Diazotrophic community Bradyrhizobium, Geobacter, Azospirillum, and Pseudodesulfovibrio had a significantly higher relative abundance in biochar treatments than in CK, which can endophytically colonize the rice roots or utilize a wide range of organic carbon sources. Our results demonstrate that biochar amendment could be a useful measure to promote soil available N pool in double rice paddies.