Under strong earthquake excitation, the structure shows nonlinear characteristics due to damage. The modified Takeda model has been widely used in the seismic simulation of civil structures because of few control parameters and precise physical meanings. However, it is difficult to identify these parameters due to their discontinuous mathematical expression. This paper proposed a modified square root constrained parameter cubature Kalman filter (MSRCP-CKF) method to identify the parameters of the modified Takeda model under the intense earthquake scenario. The proposed MSRCP-CKF method has two advantages: (1) It is derivative-free compared with standard cubature Kalman filter and has better stability of mathematical calculation. (2) The constrained parameter technique is introduced into the modified square root cubature Kalman filter to keep the physical meaning of the parameters to be identified. Numerical simulation and shaking table test of a two-story reinforced concrete frame structure demonstrate that the proposed algorithm can effectively identify the parameters of the modified Takeda model. Meanwhile the structure response is not sensitive to the stiffness yield ratio and the identification result of the stiffness yield ratio is relatively poor.