Abstract:As the public scientific research institutes are an important part of the national innovation system, the new era explores the innovative management of public scientific research institutes to meet the needs of the development of the times. At present, innovation management of China's public scientific research institutes faces practical difficulties such as weakening of management autonomy, the deficiency of academic autonomy, insufficient efficiency of science and technology services, and inadequate management tools, etc.; under the framework of the new public management theory, the restructuring of public scientific research institutes in China is promoted. The return of power, the communion of mechanisms, and the use of tools have become effective ways to solve practical problems.