Based on the requirements for advanced treatment of nitrogen in wastewater and energy conservation, the anammox-hydroxyapatite (HAP) process was applied in this study. The objective was to achieve a high efficiency of nitrogen removal at a low temperature of 7 °C. As a key influencing factor, the effect of inorganic carbon (IC) on the anammox-HAP process was examined throughout the long-term operation and in batch tests. In the long-term operation, the maximum nitrogen removal rate (NRR) reached 2.10 ± 0.09 gN/L/d at a nitrogen loading rate (NLR) of 3.0 gN/L/d. An efficient and stable nitrogen removal efficiency of 82.31 ± 2.05% was obtained at an NLR of 2.0 g/L/d. The phosphorus removal efficiency ranged from 13.65 to 54.24% as the Ca/P ratio was 1.63–5.46, and the analysis by micro characterization technologies clearly showed the formation of bio-induced HAP. It was found that IC has different effects on nitrogen and phosphorus removal under insufficient and excessive conditions. A higher addition of IC increased the anammox activity and provided the alkalinity required for the formation of HAP. However, excess IC and high calcium resulted in precipitates of calcium carbonate on the sludge surface and affected the diffusion between biomass and substrate. This hindrance to substrate transfer has impaired the anammox activity and the nitrogen removal performance. In addition, it was demonstrated that excess IC competed with phosphorus for calcium, thus having a negative effect on the removal of phosphorus. The optimal range of IC/TN was determined to be 0.25–0.58, and the influence mechanism of IC on the anammox-HAP process was clarified in this study.