Abstract: With the development of economic globalisation and the intensifying of regional integration, an urban agglomeration is becoming an important platform for international competition and cooperation. During this process, the transport facility, especially high-speed rail (thereafter HSR) acts as an essential medium for regional connectivity while generating essential impacts on the formation and optimisation of the regional spatial pattern. Using railway time data of 2008 and 2018, this paper studies the railway passenger transport service capacity of Yangtze River Delta urban agglomeration by comparing accessibility and linkage intensity level between traditional rail and high-speed rail. Based on the above investigation, this research attempts to measure how the network pattern and operational organisation mode of HSR work to reshape and develop urban spatial structure. The results are demonstrated as follows. (1) HSR has substantially shortened the travel time between cities and improved the accessibility of transport services by generating a “time-space convergence” effect, thereby leading to a shrinkage of space and time. Generally, the HSR has improved the overall railway passenger transport service capacity in the research area. The highest level of accessibility centres on the Shanghai-Nanjing channel and is declining from the core area to the peripheral region in Yangtze River Delta urban agglomeration. (2) Shanghai, Nanjing, Hangzhou, Hefei, Ningbo have formed different daily communication areas, which expand along the HSR, causing the overlapping area to increase. (3) The linkage intensity pattern in the Yangtze River Delta urban agglomeration can be characterised as multi-level and multi-core, boosting a networked regional structure. (4) By influencing urban spatial linkage, the HSR promotes regional spatial reconstruction to a large extent. The spatial structure of Yangtze River Delta urban agglomeration is expanded from the “one body two wings” structure with Shanghai as the core to the “golden triangle” structure which connects Shanghai, Nanjing, and Hangzhou. The implementation of HSR has accelerated the flow of factors, enhanced transport efficiency and promoted multi-level integrations within the agglomeration. In the future, the construction of railway corridors in marginal areas should be strengthened to expand the coverage of railway service and thus to bridge the gap in accessibility. Furthermore, it is crucial to attach importance to optimising the spatial organisation of HSR in the core area with the aim of enhancing passenger transport capacity, and encouraging the optimal allocation of resources in the region.