Based on road irregularity power spectrum of GB/T 7031—2005, the vehicle-bridge coupling vibration model with multipoint coherent stimulus input is proposed for analyzing the effect of spatial road roughness spectrum on vehicle-bridge coupling vibration. Taking the phase-lag and coherent mul-excitation into condition, a new 3D coherent excitation random vibration model for vehicle-bridge systems is proposed with pseudo excitation method(PEM). In the model, the bridge is modeled as beam-shell solid elements, the vehicle with three axles is simplied as 3D nine-degrees of freedom (DOF) model. Taking the highway beam bridge with three spans as reasearch background, the coherent effect, Phased-lag effect and consistent stimulus effect on the vibration response and spectrum characteristic of vehicle-bridge coupling system have been researched. The research demonstrates results as follow. The differences of the bridge displacement and acceleration caused by three spatial road irregularity excitation input are more obvious. The spatial road roughness spectrum has more obvious effects on the responses of car body than rear suspension. There has weak effect on the resonance frequency between vehicle-bridge coupling and road roughness spectrum. The spatial effect of road irregularity stimulus input in researching bridge-vehicle coupling should be taken into account.