With the panel data of 28 prefecture-level cities in the urban agglomeration in the middle reaches of the Yangtze River from 2006 to 2019 and the PSM-DID model, this paper studied the impacts of high-speed railway on the innovative urban development. According to the results, the opening of the HSR has a significant role in promoting the technological innovation capability in the urban agglomeration in the middle reaches of the Yangtze River. The study also finds that there are obvious temporal dynamics and regional heterogeneity in the impact of the opening of HSR on urban innovation. It’s mainly manifested in two sides. The promotion effect of the opening of HSR on urban innovation shows a trend of first rising and then falling over time. The promotion effect of the opening of HSR on innovation in large and medium-sized cities is not obvious or even negative, while the promotion effect on small cities is significantly positive. In addition, the HSR is further divided into national HSR rail and local HSR rail. The study maintains that compared with local HSR national HSR has a more significant role in promoting urban innovation.