The seismic responses of the seismic, isolation, and smart isolation systems of a mega structure were calculated and comparatively analyzed. Four groups of actual strong motion records with velocity pulses and corresponding synthetic time histories of ground motion with the same acceleration response spectra but without velocity pulses were used as ground motion inputs. Then, the influence of ground motion with and without velocity pulses on the mega structure under different control strategies was discussed. The results show that the seismic response of the mega structure's underground motion with a velocity pulse is greater than that without velocity pulse; in addition, the velocity pulse of near-fault ground motion has some negative impact on the seismic response of its seismic, isolation, and smart isolation systems. Though a mega structure with intelligent control system is more sensitive to ground motion with a velocity pulse, it can effectively reduce the displacement of the isolation layer.