The anaerobic ammonium oxidation (anammox) reaction removes nitrogen from wastewater, the performance of which is influenced by Ca2+; however, the effect of Ca2+ on microbial community structure is unclear. Therefore, the effects of Ca2+ concentration on the treatment performance of an anammox reactor and microbial community structure of anammox sludge were investigated. Ca2+ concentration minimally influenced the removal efficiency of NO2−–N and NH4+–N, but substantially influenced total N removal. Changing the Ca2+ concentration (between 25 and 125 mg/L) caused the average removal rate of total nitrogen to fluctuate by 3.3 percentage points. There were five major bacterial phyla in the anammox sludge: Proteobacteria, Chloroflexi, Acidobacteria, Planctomycete, and Chlorobi. Microbiological analysis revealed that the genera Acidobacterium, Anaerolinea, and Denitratisoma were positively correlated with Ca2+ concentration, and improved treatment performance of the anammox reactor. Moreover, uncultured Chlorobi bacterium clone RUGL1-218 (GQ421108.1) and uncultured sludge bacterium A21b (KT182572.1) may be key microorganisms for the immobilization of anammox bacteria. These findings offer a theoretical basis for improved wastewater treatment using the anammox process.