In this paper, in order to ensure stable and efficient operation of a pilot-scale modified A²/O (anoxic/anaerobic/aerobic/pre-anoxic) -MBR plant, the automatic control system based on PLC is designed and introduced from the views of system configuration and unit control methods. The master computer undertakes the monitoring and managing task by Siemens WINCC 7.0 configuring software, while the slave computer implements the function of data collection and automatic control based on Siemens S7-300 PLC. Intelligent PID algorithm is utilized to precisely control the influent flow rate, recycled flow rate and DO concentration in aerobic tank in this system. The commissioning and operation practice has proved that the PLC-based automatic control system greatly improved the degree of automation and achieved high nutrient removal efficiency in this plant.