Background harmonic source equivalent is the key to the system harmonic impedance estimation. Fluctuation quantity method, fluctua-tion normalization method and dominant fluctuation screening method to estimate the harmonic impedance is widely used in engineer-ing, but the error can not be tracked between the process of solving. In view of the above defects, this paper proposes a dual filter three point method for the estimation of the system harmonic impedance. Linear regression analysis was performed using a set of three data points. By the first screening, choose the regression error meet the accuracy of data, and then through the Nair test for the second screening, select the user side as the leading data, finally we can find the background harmonic. Through the calculation of the measured data prove that the method is correct and effective.