Previous studies have shown that the combination of inerter system and base isolation technology can reduce the dynamic response of base isolated structure under long-period ground motions. But the control effect of inerter system on inter-storey isolated structure is different from that of base isolated structure，which needs further research. The SPIS-Ⅱ inerter system is applied to the inter-storey isolated structure. The parameters of the inerter system are designed. The seismic-reduction effect of the inerter-inter-storey isolated structure under long-period ground motions is studied by numerical analysis. The results show that using the virtual excitation method to solve the random vibration response of the structure can quickly and effectively determine the parameters of the inerter system. The inerter system greatly reduces the displacement of the isolation layer，effectively solves the problem of displacement overrun of the isolation layer under long-period ground motions，and the displacement seismic-reduction ratio increases with the increase of ground motion amplitude. The inerter-inter-storey isolated system not only controls the response of the superstructure，but also further reduces the seismic response of the substructure.