The invention relates to a servo self-adaptive control system and method for a supersonic wave motor in input saturation conditions. The system comprises a pedestal and a supersonic wave motor fixing rack used for fixing the supersonic wave motor, wherein the supersonic wave motor fixing rack is arranged on the pedestal, an output shaft on one side of the supersonic wave motor is connected with a photoelectric encoder, an output shaft on the other side is connected with a flywheel inertia load, the output shaft of the flywheel inertia load is connected with a force moment sensor via a shaft coupling device, and a signal output end of the photoelectric encoder and a signal output part of the force moment sensor are respectively connected to a control system. The control system consists of a backstepping controller and a motor, a whole controller system is built based on backstepping calculation, and therefore good control effects can be obtained. The servo self-adaptive control system and method for the supersonic wave motor in the input saturation conditions put forward in the invention is high in control accuracy, simple and compact in structure and good in using effects.