The report of the 20th National Congress of the Communist Party of China proposed the integration of education, science and technology, and human resources, emphasizing the pivotal role of innovation within this framework. Universities, as crucial drivers of strategic implementation, occupy a central position. This paper, grounded in the theoretical underpinnings of the university innovation ecosystem, input-output dynamics, delves into the trajectory of university innovation through examination of innovation input, diffusion, and output. Based on the data of relevant indicators in 31 provinces, municipalities and autonomous regions, a panel model is constructed to study the university innovation system and the relationship between input, diffusion and output. The research finds that constructing a university innovation ecosystem is an urgent requirement for building an integrated university innovation system that combines education, science and technology, and human resources. Also, innovation manpower input investment serves as the cornerstone of university innovation output; innovation funding constitutes a critical safeguard for university innovation output; technology transfer plays a pivotal role in incentivizing university innovation output; and international cooperative research provides an important driving force for the innovation output of universities, but the international conference exchange has not played its due role. Based on these findings, strategic recommendations are proposed.