A non-steady-state model was developed to describe the nitrification and denitrification as well as COD removal in sequencing batch reactors (SBRs). The model was designed to discuss the effect of increasing volume by sewage feed, and the effects of changing aeration and mixing conditions during operational cycles on treatment performance. The formation and degradation of soluble organic microbial products (SMPs) were also considered in the model, because SMP is a significant organic component in biologically treated effluents. Most of the rate equations are based on the double-Monod expression and four types of biomass (heterotrophs, ammonium oxidizers, nitrite oxidizers, and inert biomass) exist in the model. Changes of GOD, ammonia and NO, during a cycle were simulated well in an 8 hour-cycle experiment using actual primary effluents. The simulation results predicted that remaining COD after 90 min mixing and 270 min aeration were almost SMP and particulate COD components. The initial concentrations of heterotrophs and nitrifiers were determined by DO consumption rate and nitrification rate of the sludge using given maximum specific substrate consumption rates. In conclusion, the model was available for discussion of effects of operational options, such as single-feed/step-feed and aeration/mixing time, on the nitrogen removal as well as organic matters.