The Harbin-Changchun City Cluster (HCCC) is an important growth engine for the revitalization of the Northeast, and it is also the main mode and spatial platform for the implementation of the new urbanization of the country. Industrial functional organization, structural upgrading and spatial transfer are important driving force for the growth of City Cluster. According to the statistical data of the employed population and industrial output value, we study the industrial spatial layout features and structural evolution of the HCCC and then explore the correlation between industrial organization and the City Cluster spatial based on the Industrial Agglomeration Indicators Analysis and the Locational Gini Coefficient. At the macro level, it is found that the industrial structure and specialized division of labor affect the spatial network and the axis pattern of the City Cluster; at the meso level, the industrial quantity and spatial distribution affect the layout of key cities and node towns in the City Cluster; at the micro level, the industrial level and transformation and upgrading affect the changes of urban spatial structure and the optimal allocation of relevant land.