An innovative shortcut biological nitrogen removal system, consisting of an aerobic submerged membrane bioreactor (MBR) and an anaerobic packed-bed biofilm reactor (PBBR), was evaluated for treating high strength ammonium-bearing wastewater. The system was seeded with enriched ammonia-oxidizing bacteria (AOB) and operated without sludge purge with a decreased hydraulic retention time (HRT) through three phases. The MBR was successful in both maintaining nitrite ratio over 0.95 and nitrification efficiency higher than 98% at a HRT of 24 h. The PBBR showed satisfactory denitrification efficiency with very low effluent nitrite and nitrate concentration (both below 3 mg/L). By examining the nitrification activity of microorganism, it was found that the specific ammonium oxidization rate (SAOR) increased from 0.17 to 0.51 g N/(g VSS·d) and then decreased to 0.22 g N/(g VSS·d) at the last phase, which resulted from the accumulation of extracellular polymers substances (EPS) and inert matters enwrapped around the zoogloea. In contrast, the average specific nitrite oxidization rate (SNOR) is 0.002 g N/(g VSS·d), only 1% of SAOR. Because very little Nitrobactor has been detected by fluorescence in situ hybridization (FISH), it is confirmed that the stability of high nitrite accumulation in MBR is caused by a large amount of AOB.