The invention discloses a harmonic and inter-harmonic separation analysis method, and the method comprises the steps: carrying out the sampling of an original electric energy signal, and carrying out the dividing of different analysis window; carrying out the windowing calculation of the original electric energy signal in each analysis window, and obtaining a windowing signal; carrying out the time domain averaging of the windowing signal, and obtaining a quasi-harmonic signal; carrying out the discrete Fourier transform of the quasi-harmonic signal, and obtaining a harmonic parameter; subtracting the quasi-harmonic signal from the original electric energy signal in the analysis windows, and obtaining a quasi-inter-harmonic signal; sequentially carrying out the windowing calculation of the quasi-inter-harmonic signal, adding zero to the tail of the sequence and carrying out the discrete Fourier transform, and obtaining an encrypted spectrum signal; analyzing the encrypted spectrum signal, and obtaining an inter-harmonic parameter. The method can accurately separate the harmonic and inter-harmonic components in one electric energy quality signal in a time domain, thereby inhibiting the spectrum interference between two sides during the analysis of the signal in the frequency domain, and improving the detection analysis precision of the harmonic and inter-harmonic.