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An inter-story shear model of asymmetric base-isolated structures incorporating deformation of each isolation bearing was built, and a method to simultaneously simulate bi-directional near-fault and far-field ground motions was proposed. A comparative study on the dynamic responses of asymmetric base-isolated structures under near-fault and far-field ground motions were conducted to investigate the effects of eccentricity in the isolation system and in the superstructures, the ratio of the uncoupled torsional to lateral frequency of the superstructure and the pulse period of near-fault ground motions on the nonlinear seismic response of asymmetric base-isolated structures. Numerical results show that eccentricity in the isolation system makes asymmetric base-isolated structure more sensitive to near-fault ground motions, and the pulse period of near-fault ground motions plays an import role in governing the seismic responses of asymmetric base-isolated structures.