Abstract: In order to study the relationship of microorganisms in bioreactor and enhance nitrogen removal, influence of pH, dissolved oxygen and applied loading on biochemical reaction and population optimizing were studied. The experimental results show that controlling loading could make two stage filters operated at the optimized conditions respectively due to population competition. Maintaining long time shortcut nitrification is not likely to be feasible when the pH value is below 8.5. Nevertheless, utilizing the characteristic that specific growth rate of ammonia oxidizer is higher than nitrite oxidizer at low dissolved oxygen concentrations, the nitrite accumulation could be up to 84% at the certain loading if the concentration of dissolved oxygen in the system is controlled below 1.8 mg/L. It is beneficial to the design of the shortcut nitrification-denitrification reactors.