In the cluster tool, it is necessary to precisely control the vacuum pressure for the wafer transportation between transport module and cassette or process modules with the range of 1*10$^{-4}$ to 5*10$^{-5}$ torr. So we have designed the pressure control system for the transport module of the cluster tool and have evaluated its performance. Digital PID is utilized with the weighted sum of both three previous errors and one current error. The feedback signal is put into the nitrogen mass flow controller using the transport module controller. This pressure control system can prevent the transport module from the particle generation and backstreaming of hazardous process gases of the process chamber.