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Harmonic distortion is an important analog performance index of the seismic data acquisition system (SDAS). A fast algorithm based on modified FFT pruning is proposed to analyze the harmonic distortion of the SDAS. The key of the harmonic distortion analysis is to compute the fundamental and harmonic components of the measured data. In this paper, a comparative analysis between the algorithm based on standard FFT and those based on single-bin DFT is performed. The calculating speed of each algorithm based on single-bin DFT is faster than algorithm based on standard FFT for harmonic distortion analysis of the SDAS. Moreover, of all the algorithms based on single-bin DFT, the modified FFT pruning algorithm is the most suitable for the harmonic distortion analysis of the SDAS with large numbers of channels.