Abstract: To build a military-civil integrated aeronautic R&D system has important significance in integrating of military and civil aeronautical scientific and technological industry, advancing aeronautical science and technologies, and influencing the market competitive structure of aeronautical scientific and technological industry. The problems of our country’s current aeronautic R&D system are the imperfects in the system that has no independent establishments respectively pursuing military and civil basic aeronautic R&D activities, and that military force has no its own aeronautic scientific and research establishments. So we should build a military-civil integrated aeronautic R&D system composed of managerial organizations, universities, military and civil basic aeronautic scientific research establishments and aviation industrial companies. Finally, we give some reform suggestions such as perfecting aeronautic R&D system, building consultation mechanism on military and civil aeronautical science research programming and management, building bid and tender institutions, and fostering military-civil integrated aviation industry corporations, etc.