Based on isolation theory, time-history analysis on isolation system with limiting displacement protective devices was studied by Fortran program. Isolation effect of non-isolated structure, isolated structure and limit isolated structure were analyzed. Adhesion phenomenon of algorithm is solved by subdividing time steps during program analysis. And it gets good effect. According to comparing with isolation effect of different isolated structure, the result that isolation effect of isolated structure and limit isolated structure is obvious is reward; and limit isolated structure can isolation and prevent large displacement of isolation layers to avoid structure failure under rare earthquake condition. So limit isolated structure plays a double protection for structure.