Seismic behavior of base-isolated structures is highly dependent on the nonlinear properties of the rubber-bearing isolated system. In this paper, a data-based method using only the partial measurements of structural dynamic response and excitation is proposed to identify the nonlinear property of rubber-bearing isolated system without mathematical model. First, structural parameters including the linear stiffness and damping of rubber-bearing under minor earthquake are identified based on the extended Kalman estimator approach. Then, nonlinear effect of rubber-bearing is treated as ‘additional unknown fictitious loading’ on the building under severe earthquake. By sequential application of Kalman estimator for the structural responses and the least-squares estimation of the ‘additional fictitious loading’, the nonlinear property of rubber-bearing can be identified. A numerical simulation results demonstrates that the proposed method is capable of identifying the nonlinear property of rubber-bearing isolated system with good accuracy.