Background and aims: Soil autotrophic microorganisms and plant primary production play crucial roles in soil carbon (C) cycling. However, the information remains limited to whether and how nitrogen (N) application influences the contribution of soil microbial C fixation to the soil organic C (SOC) pool. Methods: We investigated the effects of soil autotrophic bacterial communities on SOC storage and maize yield. A field experiment was conducted with four application rates of urea on the semiarid Loess Plateau, N application at 0 kg ha− 1 (N0), 100 kg ha− 1 (N1), 200 kg ha− 1 (N2), and 300 kg ha− 1 (N3), respectively. Results: Our results showed that SOC storage and maize yield were significantly increased by N application, but no significant SOC storage difference between N2 and N3 treatments, no further yield increase beyond 200 N kg ha− 1 application was observed. N application significantly impacted soil Calvin-Benson-Bassham (CBB) (cbbL) gene-carrying bacterial communities via changing soil pH, nitrate N, and soil water content. The diversity of soil autotrophic bacterial communities decreased with increasing rate of N application. We detected a high abundance of the autotrophic bacterial dominant genera Xanthobacter, Bradyrhizobium, Aminobacter, and Nitrosospira. The co-occurrence network of autotrophic bacteria contained four distinct modules. Structural equation modeling further indicated that the autotrophic bacterial communities had positive relationships with SOC storage and maize yield. Conclusions: Taken together, our results highlighted that N application stimulated the activity of soil autotrophic bacterial communities, contributing to an increase in SOC. The increase of SOC under N fertilization can stabilize soil fertility for maize production. [ABSTRACT FROM AUTHOR]