The urban system of the Yangtze Delta region is the largest urban complex in China. With the infrastructure connected and improving level of information integration, the effect of urban integration of internal cities is strengthening and the change of urban architecture and industrial isomorphism phenomenon will occur. At present, the hierarchical urban system of the Yangtze Delta is that Shanghai is the center, while Nanjing and Hangzhou are sub-centers. The authors calculate urban integration index through factor analysis and analyze the structure of relationship in the polycentric urban system between centers and peripheral cities through empirical data. In addition, to consider the long-term impact of initial endowment on economic activities on their own, cross-sectional OLS regression is adopted in this paper. To compare the changes in urban architecture, 2006 and 2012 data are selected in this paper respectively. The regression result indicates that the core-periphery structure of the urban system of the Yangtze Delta is significant in particular situation. By comparison, the radiation effect of secondary urban centers especially Nanjing is strengthening, and the improvement of urban integration increases the similarity of the industry and then testifies the hypothesis that the spatial structure of cities is affected by administrative barrier simultaneously.