The anaerobic ammonium oxidation (anammox) process holds great promise for treating nitrogen-contaminated water; stable nitrite-nitrogen (NO2 --N) production is significant to anammox performance. In this study, partial hydrogenotrophic denitrification (PHD) was used to stably and efficiently produce NO2 --N from nitrate-nitrogen (NO3 --N). An investigation of the effects of initial pH on the PHD process revealed that a high NO2 --N production efficiency (77.9%) could be ensured by setting an initial pH of 10.5. A combined PHD-anammox process was run for more than three months with maximal ammonium-nitrogen (NH4 +-N), NO3 --N, and total dissolved inorganic nitrogen removal efficiencies of 93.4, 98.0, and 86.9%, respectively. The NO2 --N to NH4 +-N and NO3 --N to NH4 +-N ratios indicated that various bioprocesses were involved in nitrogen removal during the anammox stage, and a 16S rRNA gene amplicon sequencing was performed to further clarify the composition of microbial communities and mechanisms involved in the nitrogen removal process.