This paper introduces a novel design of intelligent control system for a stepper motor, especially the design method of a controller for allocating pulses by using EDA technology. Which makes an excellent control on motor rotate speed and direction, and also positioning accuracy. Moreover, the controlling parameters can be changed optionally. In a word, a stepper motor with the proposed design is characteristic of its variable electroniclly controlled rotation speed, fine positioning accuracy, and simple system integration process. Finally, both the simulation and experimental results convince effectiveness of the proposed design.