A stepper motor accelerating system is used for accelerating a stepper motor from a current rotational speed to a target rotational speed. The stepper motor accelerating system comprises a controller, a pulse generator, and a driver. The controller stores a safety acceleration curve. The safety acceleration curve is defined by shifting a characteristic curve of the stepper motor with a safety margin. The controller compares the current rotational speed and the target rotational speed with the safety accelerating curve, and then gets two corresponding points on the safety accelerating curve. The controller generates a real accelerating curve based on these two corresponding points. The pulse generator receives the real accelerating curve and converts to a pulse signal. The driver receives the pulse signal, and then drives the stepper motor with the pulse signal. The present invention accelerates the stepper motor base on the safety accelerating curve. By this way, the present invention is able to prevent the stepper motor from out-of-speed or out-of-step.