Explaining the role of modern transport in realizing regional integration from the perspective of "space of flow" can provide scientific support for the interactive development of transport and urban system. Based on this, this paper uses the railway passenger data since 2000, and applies community detection algorithm to analyze the spatial organization of railway passenger transportation of the Yangtze River Delta urban agglomeration, in order to provide a new perspective for regional studies represented by transportation, and a guarantee for the study of regional integration through the rational use of railway passenger service. The conclusions can be drawn as follows: (1) We use combo community detection algorithm to divide the railway links of the Yangtze River Delta urban agglomeration into sub-groups, such as the Jinghu Community, the Zhejiang Community, the Wanjiang Community, and the Suzhongbei Community. These communities present different spatial linkage patterns and the main scope and direction of urban passenger rail links are concentrated within the community. (2) In general, the inter-community linkage is lower than the internal linkage of the community. The high internal contact community has a high degree of connection between the external communities. There is a high cross-community relationship between the railway hub cities, which forms a "core-edge" structure that does not depend on the accessibility of the railway. (3) According to the spatial characteristics, communities are divided into the single-core community, dual-core community, multi-core community, and non-core community. Different types of associations may be derived from the same type of community. During the study period, the core continued to decrease, while the higher communication channels continued to develop, connecting the main cities in each community and expanding continuously, but the channels did not match the core cities, and the transfer of core cities may occur. (4) There is a high connection between the cross-community hub cities, and the contact network is transformed from a channel point to a hub point. High-speed rails play an important role in enhancing cross-community communication and its spatial pattern changes from channel orientation to hub orientation. In the future study, it is necessary to analyze the role of different types of trains and trains in different operations. And we should combine the time cost with the number of trains, so as to more truly reflect the spatial process of urban agglomeration railway passenger transport organization.