The invention discloses an intelligent separation system and an intelligent separation method for microbes in cavity contents. The intelligent separation system comprises a press button, a controller, a display screen, a motor, a stirring device (41), a liquid adding drive device (7), a vibrating device (12), a bacterial liquid drive device (6) and at least one aspirator pump, wherein the press button is used for inputting a control signal, a control signal input end of the press button is connected with a signal input end of the controller, a signal display end of the controller is connected with the display screen, control signal output ends of the controller are respectively connected with corresponding signal input ends of the motor, the liquid adding drive device (7), the vibrating device (12), the bacterial liquid drive device (6) and the at least one aspirator pump, and an output shaft of the motor is connected with the stirring device (41). With the adoption of the system and the method, the automatic filling is realized, the content of bacteria in the impurities is reduced, the bacteria collecting rate and the purity of the bacterial liquid are improved, the odour leakage is avoided, and the treating efficiency is high.