Cities separated in space are connected together by spatial interaction (SI) between them. But the studies focusing on the SI are relatively few in China mainly because of the scarcity of data. This paper deals with the SI in terms of rail passenger flows, which is an important aspect of the network structure of urban agglomeration. By using a data set consisting of rail O-D (origin-destination) passenger flows among nearly 200 cities, intercity rail distance O-D matrixes, and some other indices, it is found that the attenuating tendency of rail passenger is obvious. And by the analysis on dominant flows and spatial structure of flows, we find that passenger flows have a trend of polarizing to hubs while the linkages between hubs upgrade. However, the gravity model reveals an overall picture of convergence process over time which is not in our expectation of integration process in the framework of globalization and economic integration. Some driven factors for the re-organization process of the structure of urban agglomeration, such as technique advance, globalization, etc. are discussed further based on the results we obtained. Cities separated in space are connected together by spatial interaction (SI) between them. But the studies focusing on the SI are relatively few in China mainly because of the scarcity of data. This paper deals with the SI in terms of rail passenger flows, which is an important aspect of the network structure of urban agglomeration. By using a data set consisting of the rail OD (origin-destination) passenger flows among nearly 200 cities, intercity rail distance OD matrixes, and some other indices, it is found that the attenuating tendency of rail passenger is obvious. And by the analysis on dominant flows and spatial structure of flows, we find that passenger flows have a trend of polarizing to hubs while the link between hubs upgrade. However, the gravity model reveals an overall picture of convergence process over time which is not in our expectation of integration process in the framework of globalization and economic integration. Some driven factors for the re-organization proce ss of the structure of urban agglomeration, such as technique advance, globalization, etc. are discussed further based on the results we obtained.