Being aim at designing a system controller used in the Noninvasive Bidirectional Positive Airway Pressure Ventilation (N-Bi-PAPV) and advancing this medical device to serve the respiratory patients who suffer from the OSAHS, COPD and etc, by using an embed ARM Microcomputer LM3S9B92, the system controller including its circuit diagram and embed software was designed in accordance with the request of Bi-PAP medical ventilator. And the ventilators critical parameters were clearly defined and ranged for this system. After testing in a spontaneously breathing simulator, this system controller may be used to control the ventilator performing function well.