Abstract: The study of the relationship between station and city is a core issue in the rapid development of China's high-speed railway (HSR) network, however, there is still relatively little relevant research on this aspect. This study explores the spatial structure characteristics of the Yangtze River Delta HSR network “flow” based on two spatial analysis units: cities and HSR stations, using complex network theory. The main findings are as follows: (1) From the perspective of cities, Shanghai, Nanjing, Hangzhou, and Hefei are in the core position of the HSR network. The Yangtze River Delta region is divided into four sub-networks, reflecting the regional closeness of the HSR network. (2) From the “station-city” perspective, the multi-station characteristics of a city can be classified into four types, and most cities generally only have one HSR station in a core position. However, there are large differences in the types of core stations. Therefore, this study suggests that the development of high-speed railway station areas should be comprehensively considered from both the perspectives of station and city. The conclusions of this study provide a useful reference value for the multi-scale and cross-scale spatial analysis of the HSR network “flow” characteristics.