Abstract: Deepening the reform of the state-owned aviation scientific research institutes is still an important strategic assignment in the 11th Five-Year Plan. Based o n an investigation, the author points out that, as a result of the reform of th e state-owned aviation scientific research institutes, the "one institution t wo systems" is indeed positive, but on the other hand does have a lot of proble ms and contradictions. When we carry on the commercialized reform in the state- owned aviation scientific research institutes, the scientific classification of the institutes is the basic point, and the "one institution two systems" is th e transitional type of reform. At the same time, creating a series of good polic y environment for the reform is necessary.