The university science and technology innovation system is an essential bridge between higher education and national innovation development. Since the founding of the Communist Party of China, the scientific and technological innovation system of Chinese universities has intermingled with the historical environment and internal and external factors and has gone through several stages of development from weak to strong and from fragile to solid. In this process, the Communist Party of China has always been firmly based on the central concept of people-oriented, using a forward-looking vision to develop the macro deployment of the university science and technology innovation system and finally using the combination of ideology and politics, the three-wide education throughout the sustainable development, and optimization of the system, returning to the “university” nature of the university science and technology innovation system, to achieve the fusion of the system and the Party-building development. To this end, the university science and technology system in the new era must continue to uphold the leadership of the Communist Party of China, draw on the power of the three chains led by the Party, inductively form contemporary inspiration from the logic of construction over the past century, and adapt to the complex and changing world situation of the future.