Transportation infrastructure and innovation play an important role in promoting regional economic growth. However, previous studies have mainly focused on the economic agglomeration by increased accessibility, but ignored the important on inter-city economic linkages and the network externalities it generated. Based on the externality perspective, this paper uses the propensity score matching model (PSM-DID) and spatial econometric model to analyze the heterogeneous impact of HSR opening on urban innovation performance and compare the differential effects of agglomeration externalities and network externalities on knowledge spillovers. The empirical results suggest the following: (1) The opening of HSR significantly improves urban innovation performance, but there is significant spatial heterogeneity. (2) The opening of HSR not only promotes the agglomeration of production factors to cities, but also strengthens inter-city economic connections, thus improving urban innovation performance through agglomeration externalities and network externalities. However, compared to agglomeration externalities, network externalities have a superior strength of impact on urban innovation performance. (3) From the dynamic effect perspective, the opening of HSR has a hysteresis effect on urban innovation of 2-3 years, and differences exist between cities.