This paper deeply discusses the urgency and implementation strategy of innovative scientific research management system. Under the background of the rapid development of science and technology, the traditional scientific research management system has been stretched thin, and it is difficult to meet the diversified and efficient needs of scientific research activities. Therefore, we urgently need to review and reform the existing scientific research management system. Firstly, this paper objectively analyzes the shortcomings of the current scientific research management system, as well as the challenges and difficulties it faces, and then leads to the urgency and necessity of innovating the scientific research management system. On this basis, the paper deeply analyzes the theoretical foundation of the innovative scientific research management system, and combines the advanced practice in this field at home and abroad to provide us with valuable reference. More importantly, the paper puts forward a series of practical strategies and suggestions, such as building a diversified scientific research investment mechanism, optimizing the scientific research evaluation system and incentive mechanism, and strengthening the construction of scientific research ethics and study style, so as to provide powerful theoretical support and practical guidelines for the innovation of scientific research management system.