Owing to the enhanced accessibility afforded by high-speed rail, the relationship between megacities and their neighboring cities has grown closer. Megacities exert a significant influence on the land use of neighboring cities. This study employs a spatial econometric model to investigate the direct impact and spatial spillover effects of high-speed rail on urban land values, based on urban panel data from China’s Yangtze River Delta region (2006-2020). The results revealed that shorter commuting times and improved frequency of service had a more substantial effect. Additionally, due to alterations in land values, there is a distinct preference tendency for urban land use attributes. Therefore, the city’s spatial organization has transformed, and its center of gravity has shifted as well. This study provides crucial theoretical justifications and empirical evidence to fill the gaps left by previous research on the effects of short-haul high-speed rail commuting on urban housing prices and land use. The study also offers valuable insights for strategic planning and implementation aimed at promoting urban development and urban agglomeration construction through HSR construction.