The improvement of scientific research in universities is crucial to the construction of an innovative country in China new era. By describing the historical evolution of scientific research in Chinese universities and finding that there are bottlenecks in current Chinese university scientific research, such as role positioning deviation, R&D investment structure imbalance, relatively lagging basic research, and low market coupling. Furthermore, it is pointed out that the role change of scientific research in universities is urgent. Basic research should be taken as the core function of scientific research in universities, fostering an atmosphere of bold trial and error innovation, and supporting technological innovation and applied research and development with basic research. Therefore, from the four aspects of improving the efficiency of the use of scientific research funds, strengthening basic research and independent research and development capabilities, coupling the market application of scientific research results, and optimizing scientific research talent cultivation mechanisms, the optimization path driven by scientific research innovation in universities is proposed.