In this paper, a system identification approach is proposed for high-rise building under unknown seismic excitation with limited output measurements. A high-rise building is decomposed into small size substructures based on its finite element formulation. Interaction effect between adjacent substructures is considered as ‘equivalent known inputs’ to each substructure. Unknown seismic excitation is considered as ‘equivalent unknown inputs’ at the first floor. By sequentially utilizing the extended Kalman estimator for the extended state vectors and the least squares estimation for the ‘equivalent unknown inputs’, structural parameters above the first story of a shear building can be identified. Then, with the analysis of the measured absolute acceleration responses in frequency domain and the peak-picking method for the estimation of the first natural frequency of the building, structural parameters of the first story can be identified from the frequency equation. Finally, the unknown seismic excitation can be identified via the numerical solution of a first-order differential equation. It is shown by a numerical example that the proposed method can identify high-rise building parameters and the seismic excitation with good accuracy.