In this work, a mathematical model including both ammonium oxidizing bacteria (AOB) and heterotrophic bacteria (HB) is constructed to predict N2O production from the nitritation systems receiving the real anaerobic digestion liquor. This is for the first time that N2O production from such systems was modeled considering both AOB and HB. The model was calibrated and validated using experimental data from both lab- and pilot-scale nitritation reactors. The model predictions matched the dynamic N2O, ammonium, nitrite and chemical oxygen demand data well, supporting the capability of the model. Modeling results indicated that HB are the dominant contributor to N2O production in the above systems with the dissolved oxygen (DO) concentration of 0.5–1.0 mg O2/L, accounting for approximately 75% of N2O production. The modeling results also suggested that the contribution of HB to N2O production decreased with the increasing DO concentrations, from 75% at DO = 0.5 mg O2/L to 25% at DO = 7.0 mg O2/L, with a corresponding increase of the AOB contribution (from 25% to 75%). Similar to HB, the total N2O production rate also decreased dramatically from 0.65 to 0.25 mg N/L/h when DO concentration increased from 0.5 to 7.0 mg O2/L.