Based on the urban high-speed rail sites data matching the R&D data of listed companies from 2008 to 2018， the impact of high-speed rail hub on enterprise innovation output and its intermediary mechanism from the perspective of the geographical peer effect are empirically studied. The findings are as follows: First, the high-speed rail hub has an inhibitory and dynamic effect on enterprises’ innovation output. Second, by promoting the flow of innovative elements, high-speed rail hub enhances the geographical peer effect in innovation, and hence restrains enterprises’ innovation. Third, non-state-owned enterprises and small enterprises are more susceptible to the suppression effect because of the reduction of competitive pressure caused by the improvement of high-speed rail and the peer effect. Fourth, there are obvious spatial gradient difference in the impact of high-speed rail hubs on enterprises’ innovation output. In the central region, non-provincial capital cities and less-developed areas, the negative impact is more significant, while the promotion effect is mainly in the innovative cities.