In order to solve the problems of fence effect and spectral leakage in Fast Fourier Transform analysis, an approach of high accuracy harmonic analysis is proposed, which bases on 5-term Maximum-Sidelobe-Decay window and triple-spectrum-line interpolation. It analyzes the window function and other commonly used window function in terms of time and frequency domain, reflecting the excellent characteristics of the sidelobe in the window function. It uses the cftool tool in Matlab to fit the modified formula of the algorithm. Then, it analyzes the general signal and signal of frequency change with the method, comparing with other several commonly used window function and interpolation algorithm results, this method shows a higher accuracy performance. In high accuracy analysis of harmonic algorithm based on 5-term MSD window and interpolation, the relative error of the amplitude has reached 10^-9%, and it also has a good performance when frequency fluctuation happens.