The dynamics model of Alcaligenes faecalis NR was combined with the activated sludge model No. 1 to guide how to make the bioaugmentation of strain NR successful. Model studies show that conventional heterotrophic bacteria in activated sludge always outcompete strain NR. The competition between strain NR and Nitrosomonas, a typical ammonium-oxidizing bacterium (AOB), mainly depends on COD concentration and maximum growth rate of Nitrosomonas. 2000 mg/L of COD ensures that strain NR is always able to outcompete AOB. A biofilm reactor was developed to avoid a quick decrease in influent substrates. Approximately 94.2% of TN and 93.6% of COD were removed in the bioaugmented biofilm reactor, showing much better performance than an identical biofilm reactor without strain NR inoculation. A long-term experiment showed that strain NR successfully proliferated in the bioaugmented reactor. The abundance variation of strain NR mainly depended on influent COD concentrations, which was consistent with the model results.