China’s university science and technology parks (USTPs) were established with the aim of closely combining the scientific and educational intellectual resources of universities with the advantageous innovation resources of the market to form a fusion of industry and education. This paper uses the establishment of national university science and technology parks (NUSTPs) as a “quasi-natural experiment.” We used the panel data of 293 cities from 1999 to 2017 as a sample to analyze the impact of NUSTP establishment on urban innovation, using the difference-in-difference method. The research found the following: (1) The establishment of NUSTPs significantly improves the level of urban innovation, and the conclusion is still valid after a series of robustness tests. The urban innovation effect of the establishment of NUSTPs is dynamic, non-lagging, and continuous. (2) The innovation effect differs significantly, depending on the city region, the city scale, and the university level. Specifically, the innovation effect of the establishment of NUSTPs is significant for cities in middle and western cities, large-scale cities, and cities with double first-class and local universities setting up USTPs, while the effect is not significant for cities in eastern cities, small- and medium-scale cities, and non-double first-class and ministry-affiliated institutions. (3) The impact mechanism test shows that NUSTPs contribute to urban innovation by increasing the city’s human capital, enhancing the degree of industrial agglomeration, and creating an innovation space effect.