The analysis of transport networks is an important component of urban and regional development and planning. Based on the four main stages of China’s railway development from 2008 to 2017, this paper analyzes the hierarchical and spatial heterogeneity distribution of train flows. We found a high degree of spatial matching with the distribution of China’s main railway corridors. Then, using a classical community detection algorithm, this paper attempts to describe the functional structure and regional effects of China’s railway network. We also explore the impacts of construction policies and changes to train operations on the spatial organizing pattern and evolution of network hierarchies. The results of this empirical study reveal a clear pattern of independent communities, which in turn indicates the existence of a hierarchical structure in China’s railway network. The decreases in both the number of communities and average distance between community centers indicate that the newer high-speed rail services have shortened the connections between cities. In addition, the detected communities are inconsistent with China’s actual administrative divisions in terms of quantity and boundaries. The spatial spillover and segmentation effects cause the railway network in different regions to be self-contained. Finally, the detected communities in each stage can be divided into the categories of monocentric structure, dual-nuclei structure, and polycentric structure according to the number of extracted hubs. The polycentric structure is the dominant mode, which shows that the railway network has significant spatial dependence and a diversified spatial organization mode. This study has great significance for policymakers seeking to guide the future construction of high-speed rail lines and optimize national or regional railway networks.