Abstract: To investigate the influence of the near-fault vertical ground motions on the seismic behavior of reinforced concrete (RC) double-deck viaduct, a three-dimensional numerical seismic analysis model for a 5-span double-deck viaduct was built. And the accuracy of the numerical method was verified. A total of 40 sets of near-fault ground motions with obvious velocity pulse component were selected from the PEER database. Dynamic time history analysis was conducted for the viaduct model under two working conditions: horizontal seismic motions only, and horizontal + vertical seismic motions simultaneously. The seismic responses of the viaduct under these two conditions were analyzed and compared with each other. The results indicate that, compared with the response of the viaduct under horizontal motions only, the response of the viaduct under combined horizontal and vertical motions increases obviously. The maximum deformations of the upper and lower floor bearings increase by 33% and 28%, respectively. And the maximum deformations of the upper and lower floor shear keys increase by 36% and 35%, respectively. The axial load change ratios of the upper and lower floor piers increase by 85% and 38%, respectively. The risk of the piers suffering tensile load will increase obviously under the near-fault vertical ground motions. While the motions have little influence on the curvature ductility factors of the pier sections. The bearings of the double-deck viaduct will suffer slight or moderate damage, the shear keys will suffer severe or complete damage under the near-fault ground motions. And the upper floor bearings and shear keys are more vulnerable than the lower floor bearings and shear keys. The research results in this paper provide guidelines for the seismic design and retrofit of double-deck viaducts in high intensity zones.