A systematic method is developed for the dynamic analysis of the structures with sliding isolation which is a highly non-linear dynamic problem. According to the proposed method, a unified motion equation can be adapted for both stick and slip modes of the system. Unlike the traditional methods by which the integration interval has to be chopped into infinitesimal pieces during the transition of sliding and non-sliding modes, the integration interval remains constant throughout the whole process of the dynamic analysis by the proposed method so that accuracy and efficiency in the analysis of the non-linear system can be enhanced to a large extent. Moreover, the proposed method is general enough to be adapted for the analysis of the structures with multiple sliding isolators undergoing independent motion conditions simultaneously. The superiority of the proposed method for the analysis of sliding supported structures is verified by a three-span continuous bridge subjected to harmonic motions and real earthquakes. In addition, the side effect of excessive displacement of the superstructure induced by the sliding isolation is eliminated by replacing one of the roller supports on the abutments with hinge support. Therefore, both reductions in the forces of the substructure and the displacements of the superstructure can be achieved simultaneously.