Accurate identification of the existing city structure is crucial in urban management. The regional overlapping pattern within cities indicates the diverse residential activities of city areas. However, previous studies have neglected the importance of overlapping regions. Based on taxi trajectory data from Wuhan, China, this study constructs a spatially-embedded network model and introduces the network science into the analysis of inter-city spatial interactions. The community detection method is used to reveal the overlapping city structure, and a variety of indicators are used to investigate the characteristics of overlapping city areas. Accounting for the differences between short- and long-distance travel, this study reveals the four-storey overlapping city structure. Further exploration of the urban structure shows that the overlapping areas identified by different track lengths show significant heterogeneity in their function, and the overlapping areas support more of the basic needs of daily life during short trips. This study also explores the importance of overlapping urban communities under the current structure, which supports the development and implementation of urban transport and infrastructure layout policies. The hierarchical and overlapping structures revealed in this study explain the activities of residents activities better than administrative divisions.