Aiming at the problem that background harmonic voltage fluctuation affects harmonic impedance estimation, a system harmonic impedance estimation method based on three-point screening and partial least squares is proposed. Based on the phase angle relationship between each measurement and estimator, a set of three-point data is used to establish the equation. According to the discriminant, the measured voltage and current data of the common coupling point when the background harmonic voltage is stable are screened out. Then the partial least square method is used to estimate the harmonic impedance of the AC system. The simulation results show that the proposed method is correct and effective, and can reduce the influence of background harmonic voltage fluctuation on the harmonic impedance of the system. Compared with the traditional method, the estimation accuracy is higher.