In this paper, we apply Fourier Spectral Element Method (SEM) to the dynamic analysis of large dams, and take advantage of its high numerical accuracy and exponential rate of convergence and excellent geometrical adaptability to improve the computational procedure, efficiency and results of dynamic problem of large dams in numerical calculation. Based on the governing dynamic equation of large dams with the boundary nonlinearity, this paper derives the Fourier spectral stiffness, mass, damping matrix and equivalent load vector in terms of discrete Fourier spectral series, so a spectral formulation of dynamic analysis of large dams can be reached. For the purpose of higher numerical efficiency, Fast Fourier Transform (FFT) is also adopted in this paper. Although SEM has few applications in the analysis of solid structures, this paper indicates that SEM could be used in solid construction such as large dams as good as other preferable fields.