A modified version of the IAWQ activated sludge model No. 1 (ASM 1) is adopted for the simulation of a sequencing batch reactor (SBR) to optimize the removal of nitrogen (T-N) and organic matters (COD) from wastewater. Since the removal of nitrogen requires both aerobic nitrification and anaerobic denitrification, we seek to find the optimal strategies of substrate fill and aeration. Substrate filling strategy critically influences the removal efficiency of T-N and COD; one fast discrete fill in the beginning of a cycle leads to the best result, while a slow continuous fill results in poor nitrification. In addition, the total aeration time is more important for the removal efficiency than the aeration frequency. A short aeration is beneficial for T-N removal, while a long aeration is beneficial for COD removal as expected. As a result, there is an optimal condition of aeration for the simultaneous removal of T-N and COD.