The invention discloses a rear-stage pump control system and control method for a vacuum system. The rear-stage pump control system comprises a vacuum chamber, a rear-stage pump, a front-stage pump, an electric control valve, a vacuum sensor and a control unit, wherein a gas pumping port of the rear-stage pump communicates with the vacuum chamber, and a gas exhausting port of the rear-stage pump communicates with a gas pumping port of the front-stage pump through the electric control valve; and a signal input interface of the control unit is connected with the vacuum sensor and a built-in temperature sensor of the rear-stage pump, and a control output interface of the control unit is connected with a front-stage pump controller, a rear-stage pump controller and an input interface of an electric control valve controller. According to the rear-stage pump control system and control method for the vacuum system, by arranging the control unit, the front-stage pump and the rear-stage pump can be controlled to be started/stopped in real time conveniently, the rotating speed of the rear-stage pump can be adjusted conveniently, the vacuum degree of the vacuum chamber and the working temperature of the rear-stage pump are measured in time, the pumping speed of the rear-stage pump can be adjusted conveniently, the service life of the rear-stage pump is guaranteed, the working stability ofthe rear-stage pump is guaranteed, and power consumption is reduced; and the whole vacuum system has the advantages of being small in size and high in pumping speed, integration of the whole vacuum system is facilitated, and compared with a front-stage pump peripheral mode, the gas circuit structure is simplified.