Abstract:The urban hierarchy system is the spatial mapping of the technical hierarchy system. The formation process of the innovation network is the interaction process that the radiation effect of innovation centers and the construction of inter-city innovation spatial correlation between cities. It has a significant impact on the improvement of the innovation ability of urban agglomeration. This paper selects the panel data of Yangtze River Delta Mega-city Region from 2005 to 2016, and divides the distance factors into three dimensions: spatial distance, technical distance, and economic distance. It explores the path of proximity effect on the innovation system of urban agglomerations and explores the different role of innovation centers at different hierarchy rank. The results show that the proximity effect has a significant impact on the improvement of the innovation capacity of urban agglomeration. The significance of spatial proximity, technological proximity, and economic proximity is different, which forms a differential effect on the intensity and direction of innovation spillover effects. Therefore, to expand the role of proximity effect, the paper puts forward the countermeasures from the aspects of improving the infrastructure network and optimizing the coordination of innovation policy in urban agglomeration, so as to promote the synergetic development of urban agglomerations.