A shaking table test model of a mega-sub structural system is carried out in order to study the dynamic performance of this system when subjected to near-fault ground motions with velocity pulse. Test specimens are designed and produced， called aseismic model and isolation model， respectively. Two groups of actual strong motion records with velocity pulse and corresponding synthetic time histories with same response spectra and without velocity pulse are used as ground motion inputs. Moreover， the simulation analyses of the test models are carried out by SAP2000 software. Numerical simulation results are compared with the experimental results. The results shows that there are some differences between the numerical and experimental results， but the trends are consistent with each other. Both simulated and experimental results demonstrate that the seismic responses of the mega-sub aseismic system and mega-sub isolation system under ground motions with velocity pulse are greater than that without velocity pulse. In addition， the responses of the mega-sub isolation system are less than that of the mega-sub aseismic system， and it has good shock absorption effect.