Accelerating the transformation and application of national defense intellectual property is a powerful measure to implement the innovation-driven development strategy and the civil-military integration development strategy. The national defense intellectual property legal system has obvious fragmentation characteristics, and the construction of the legal system lags behind the actual needs of national defense intellectual property rights transformation. The administrative management system originated in the era of planned economy has gradually restricted the innovation and development of national defense technology. The problem that the national defense intellectual property legal system and the management system are not coordinated and mutually restricted is the root of the two's inability to effectively coordinate. It is necessary to achieve effective coordination and benign development of the legal system and the management system by improving the legal system, clarifying the rights and obligations of the subject, strengthening the coordinated management of the military and the civil, and improving the conversion efficiency.