The present invention provides a system for compensating for disturbances of a motor driving a power steering motor. The system for compensating for disturbance of a motor driven power steering compensates for the disturbance using a closed-loop based input value prediction model unit, predicts an input value from a command by the closed-loop based input value prediction model unit alone, and compensates for the disturbance according to a required disturbance frequency band when there is a difference between the predicted input value and the input value error-compensated by a feedback controller.