A novel four‐stage pilot‐scale anaerobic/anoxic/oxic/oxic (A2/O2) biofilm process was successfully developed to treat coking wastewater with high ammonium loading. In this study, three different dynamical models including the first‐order substrate removal model, the Monod‐biological contact oxidation (Monod‐BCO) model, and the modified Stover‐Kincannon model were particularly applied to analyze kinetics of ammonium removal in a two‐step aerobic stage. For the O1 reactor, all models were appropriate for describing ammonium removal and the correlation coefficients of first‐order substrate removal model, BCO model, and modified Stover‐Kincannon model were 0.8974, 0.9210, and 0.9726, respectively. The model verification indicated that the modified Stover‐Kincannon model was slightly more applicable to predict ammonium removal in the O1 reactor. It was demonstrated that the maximum removal rate of ammonium was 0.208 kg/(m3 · d) by the Stover‐Kincannon model. For the O2 reactor, the modified Stover‐Kincannon model turned out to be the best fitting kinetic model for ammonium removal compared to the first‐order substrate removal model (R2 = 0.1556) and Monod‐BCO model (R2 = 0.5022). The maximum ammonium conversion rate (Um2‐O2) by the modified Stover‐Kincannon model was 1.180 kg/(m3 · d), while saturation rate constant k3‐O2 was 1.221 kg/(m3 · d). Furthermore, the determination coefficient between measured and predicted values obtained by the modified Stover‐Kincannon model was quite high (R2 = 0.9788) in the O2 process and a lower average residual square (6.60 × 10−6) was also obtained. The results of kinetic studies by the Stover‐Kincannon model can predict ammonia removal efficiency well in two‐step aerobic biofilm reactors of a coking wastewater treatment combined system.