Scientific and technological innovation is the first driving force for development. With the development of modern science and technology entering the era of Magscience, the paradigm of scientific and technological innovation has changed, and the interdisciplinary integration and the transformation of Industry-University-Research cooperation achievements have become the trend. In the new era, it requires the systematic management methods to improve China"s scientific and technological innovation management system, in order to guide researchers to meet the national strategic needs, pay attention to the "bottleneck" problem, conduct original exploration and research, and further improve the level of China"s scientific and technological innovation. Based on the SPIO model, this study systematically analyzes the existing problems of the scientific and technological innovation management system from the four dimensions of structure, process, input and outcome, and puts forward a series of suggestions for improvement and optimization, which provides basic ideas for Chinese scientific research management decision-making departments and related scholars to carry out theoretical research and practical exploration.