This study examines the spatiotemporal variability of high-speed rail (HSR) effects on the agglomeration of secondary and tertiary sectors in China. A Geographically and Temporally Weighted Regression (GTWR) model is utilized to examine the varying impacts of HSR operation (HSR dummy), accessibility (Weighted Average Shortest Travel Time, WATT), and connectivity (WDC) across different regions, city scales, and major urban agglomerations, using panel data from various cities for the period 2008–2019. The findings indicate considerable spatiotemporal non-stationarity in the impact of HSR on industrial agglomeration. In the secondary industry, HSR typically promotes dispersion nationally while simultaneously fostering agglomeration in the more developed eastern coastal regions. The effects on the tertiary sector are intricate, demonstrating a dynamic temporal pattern of initial dispersion followed by agglomeration, significantly influenced by regional development phases and city scales. The results highlight how HSR transforms China’s industrial spatial distribution by modifying transportation expenses, market accessibility, and knowledge spillovers, offering an empirical foundation for developing tailored regional transportation and industrial strategies.