Model updating is an important work in structural damage identification, mostly using finite element model, but refined modeling usually leads to computational inefficiency. In this paper, an effective spectral element model is proposed for reinforced concrete (RC) T-beam. Firstly, the displacement governing equations were derived by using Hamilton principle, the displacement field was transformed from time domain to frequency domain using Fast Fourier Transform (FFT). The spectral element model of RC T-beam was established, and a nonlinear static calculation framework was developed. In order to verify the validity of the model presented in this paper, a RC T-beam specimen was experimental tested and numerical simulation was carried out using finite element model. Finally, the structural damage identification based on model updating was carried out by using the proposed spectral element model. It shows that only 34 spectral elements were used to complete the calculation, thus, the computational efficiency of the spectral model is much higher than finite element model. Fast convergence can be achieved by using the spectral element model. In summary, the proposed spectral element model can be applied in model updating, which provides a reliable tool for structural health monitoring and damage identification.