As the nitrogen discharge limit gets more stringent, ammonium and nitrate residual in the effluent of mainstream deammonification process are becoming an issue that need to be addressed. Thus, developing a post-deammonification polishing process is necessary to promote the implementation of mainstream deammonification. In this study, a final polishing process coupling anammox with partial denitrification is proposed to simultaneously remove ammonium and nitrate, and the long-term (120 days) impact of carbon type and COD/N ratio on promoting partial denitrification was evaluated. Results suggested that acetate and glycerol displayed a good potential for promoting partial denitrification. However, methanol showed challenges of establishing efficient partial denitrification in long-term operation. The key factor for a successful concurrent operation of anammox and partial denitrification lies on controlling the balance between denitrifier rate and AnAOB rate to simultaneously remove residual ammonium and nitrate.