Inorganic carbon (IC) is important for anaerobic ammonium oxidation (anammox). In this study, the effects of the IC concentration on N2O emissions and microbial diversity in an anammox reactor were investigated. N2O emissions were positively correlated with IC concentrations, and IC concentrations in the range of 55-130 mg/L were optimal, considering the nitrogen removal rate and N2O emissions. High IC concentrations resulted in the formation of CaCO3 on the surface of anammox granules, which impacted the diffusion conditions of the substrate. Microbial community analysis indicated that high IC concentrations decreased the populations of specific bacteria, such as Achromobacter spanius strain YJART-7, Achromobacter xylosoxidans strain IHB B 6801, and Denitratisoma oestradiolicum clone 20b_15. D. oestradiolicum clone 20b_15 appeared to be the key contributor to N2O emissions. High N2O emissions may result from changes in organic carbon sources, which lead to denitrification by D. oestradiolicum clone 20b_15.