System harmonic impedance’s accurately measurement is the key to hierarchical quantification on harmonic distortion of point of common coupling. The classic approach has large errors for the fluctuations of the background harmonic. Based on a strong linear correlation between the point of common coupling of the harmonic voltage and current fluctuations, when background harmonic has no fluctuation, proposed a method on the basis of the correlation filtering principle to calculate system harmonic impedance, introducing the "coefficient of determination" as the criterion, selecting the periods of the corresponding samples when the background harmonic is relatively stable, using the ratio of the fluctuating quantity to calculate system harmonic impedance. Simulation and practical engineering examples show that the method improves the accuracy of harmonic impedance, more accurately and effectively to achieve the hierarchical quantify the amount of harmonic distortion.