Abstract: At present, China's patent protection law about Chang'e Project mainly involves the ownership system, the incentive mechanism, the management mechanism and the patent application process. However, with the reform of scientific research system of the national defense in China and the market operation of Chang'e Project, the existing patent protection system has such problems as the lack of patent protection of scientific research institutes, the insufficient protection of the inventor's rights and interests, the poor coordination of the management institutions and unreasonable patent application process. The improvement of the patent protection system of Chang'e Project must start from the explicit patent ownership, the incentive of innovation enthusiasm of the project undertakers and the improvement of the mechanism of patent management and transformation. At the same time, the improvement of the patent protection system should ensure the leading role of the aerospace patent for the national economic and social development ant it should also improve the international protection level of the Chang'e Project patent by perfecting the supporting laws of intellectual property rights protection in international cooperation.