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Different from the fast Fourier transform-based method, the frequency shifting and filtering (FSF) algorithm employs only a few simple operations in the time domain for harmonic analysis. However, the systematic error of FSF caused by the imperfect performance of the low-pass filter is ignored. In this paper, a novel smoothing frequency shifting and filtering (SFSF) algorithm is proposed. First, the systematic error of FSF is modeled. Then, the SFSF-based harmonic analysis with systematic error compensation is presented. Finally, the features of the SFSF are discussed. Simulation shows good agreement with the theoretical results. Results of simulations and experiment confirm that the SFSF method can perform harmonic analysis accurately.