Abstract: Based on the status quo of the development of metropolitan area innovation system, the urban agglomeration has formed a hierarchical structure and geographic accessibility produces material consequences for the spatial structure. Firstly, the main points about the spatial structure theory on the research of metropolitan area innovation system are reviewed, the conception of city technological potential is put forward. Seceondly, the key model of the spatial interaction theory, the potential model, is introduced and its applicability and extensibility to calculation of the city technological potential are explained. Yangtze River Delta is taken as a case to calculate the city technological potential and analyze the hierarchy accordingly. The difference between the case study and planning indicates that the hierarchy of the metropolitan area innovation system should be brought out by market rather than the result of administrative instrument.