The invention belongs to the field of aquaculture engineering and particularly provides an automatic high-density cultivation system and method for rotifers. The system mainly comprises a source water treater, an ultrasonic sterilizer, an aquaculture tank, a microfiltration device, a water storage tank, an oxygen generator, an air pump, a booster pump, water level sensors, an electronic controller and the like. The method comprises steps as follows: when the system starts a water changing process automatically or manually, water enters the microfiltration device through solenoid valves and an air-lift pipe in sequence, meanwhile, the water level sensors are triggered, a drive motor, a back washing pump and the air pump are started, the rotifers and resting eggs are filtered by the microfiltration device and then flow back to the aquaculture tank, aquaculture wastewater containing excrement waste is discharged into a drain tank and flows out of the system through an overflow port after secondary filtration, when water level in the aquaculture tank is reduced to cause re-triggering of the water level sensors, the solenoid valves are closed to stop water discharge, a water supplementing program is started until the water level returns to normal, and the process enters a next countdown cultivation period. Key parameters of the system can be set manually, and automatic high-density cultivation of the rotifers can be realized.