In this research, the target process was a modified type of a conventional aeration tank with four different influent feeding points and alternated aeration to obtain nitrogen removal. For more accurate switching of influent feeding, the process was operated under a designed control strategy based on monitoring of NH4-N and NOX-N concentrations in the tank. However, the strategy did have some limitations. For example, it was not sensitive to detecting the end of each reaction when losing the balance between nitrification and denitrification of each opposite part of biological tank. To overcome the limitations of the existing control strategy, a diagnosis-based control strategy was suggested in this research using the diagnosis results classified as normal (N), ammonia accumulation (AA) and nitrate accumulation (NA). Using the pre-designed rules for control actions, the aeration and volume of the aerated part of the reactor could be increased or decreased at a fixed mode time. In simulations of the suggested diagnosis-based control strategy, the NH4-N and NOX-N removal rates in the reactor were maintained at higher levels than those of the existing control strategy.