Taking a cable-stayed bridge with high-low towers as the research object, the large mass method is employed to simulate non-uniform excitation for seismic response analysis. The seismic response of cable-stayed bridge with high-low towers under pulse-type near-fault earthquake considering traveling wave effect under different longitudinal constraint systems was studied. The effect of traveling wave on seismic response of cable-stayed bridge with high-low towers under different ground motion types and ground motion propagation directions was discussed. The variation of seismic response of cable-stayed bridge with pulse period under different pulse period ground motion was analyzed. Results show that the seismic response of cable-stayed bridge with consolidation system is more sensitive to the change of apparent wave velocity than that of cable-stayed bridge with longitudinal damping system and semi-floating system. The influence of traveling wave effect in different seismic input directions on the seismic response of cable-stayed bridges differs. When the apparent wave velocity is low, the difference of internal force between high tower and low tower is greatly influenced by the apparent wave velocity. The seismic response of cable-stayed bridge with longitudinal damping system increases first and then decreases with the increase of pulse period. The variation of the internal force at the bottom of the tower with the apparent wave velocity is significantly affected by the pulse period. When the apparent wave velocity is high and the pulse period is close to the longitudinal first-order period of the cable-stayed bridge, the seismic response of cable-stayed bridge reaches the maximum.