Abstract: The main objective of this paper is to present a more reasonable numerical method for the time-history analysis of base-isolated structures. A nonlinear hysteretic model of elastomeric bearings is incorporated into a general nonlinear dynamic analysis program HBTA (Highrise Building Time-history Analysis). Biaxial nonlinear displacement behavior of elastomeric bearings under biaxial horizontal seismic forces is taken into consideration in the updated program. Different damping ratios are adopted to describe the damping behavior of the Upper-RC-stories and the bottom-elastomeric-isolation-story of the base-isolated structures. Based on the step-by-step integration method and the Wilson'θ method, a new solution algorithm suitable for base-isolated structures is presented, which can perform the time-history integration of two sub-structures simultaneously. From the dynamic analysis results of an eight-story-base-isolated reinforced concrete structure, it is concluded that the consideration of the difference of damping ratios in the structures is necessary.