The influence of traveling wave on the seismic response of long-span double-deck cable-stayed bridge, especially taking into account the web members between decks, has not been studied thoroughly. Shanghai Minpu Bridge, which is the longest double-deck long-span cable-stayed highway bridge, is taken as an example to study the traveling wave on the seismic response in this paper. Finite element model with beam and shell element is established, in which the web members between decks are also modeled. Initial equilibrium configuration for the bridge is acquired through nonlinear static analysis. The modal analysis and geometric nonlinear dynamic analysis are carried out based on the initial equilibrium configuration to get the dynamic characters and seismic responses respectively. The influence of traveling wave on the seismic response is demonstrated by three groups of earthquake motions with different apparent wave velocities. The effect of apparent wave velocities on the seismic response of tower, subsidiary piers and the relative displacement between tower and girder and between subsidiary piers and girder are discussed in detail. It is concluded that the seismic responses of double-deck long-span cable-stayed bridges depend heavily on the apparent wave velocities and the earthquake motions inputted. Therefore the selection of a ppropriate earthquake motions and the determination of reasonable apparent wave velocities are of much importance to seismic response of bridges.