Abstract To date, comparative research of multiple urban networks are constantly emerging, but the relationship between virtual networks and physical networks still remains a riddle to be discovered. To step into this field, we used flight data and patent transaction data of prefecture‐level cities in China from 2010 to 2015 to construct the aviation network and the innovation network. After conducting a comparative study, we found that the structure of these two networks is different: the aviation network is a “hub‐and‐spoke network” structure while the innovation network is a diamond‐shaped structure; the spatial organization pattern of the aviation network is decentralized, while the innovation network shows a high geographic agglomeration; furthermore, the connectivity of the aviation network contributes to the balanced regional development, but that of the innovation network shows a preferred trend, with more concentration given to the development of eastern China. Finally, we also found that the innovation network and the aviation network are not completely interdependent, which reveals that the coupling relationship between the “virtual network” and the “physical network” in the urban network is also affected by other factors.
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