This paper reports a new method to estimate the system-side harmonic impedance and the customer-side harmonic voltage emission level at the point of common coupling（PCC） in a power grid based on the covariance characteristic of random vectors. Since the harmonic current at the PCC commonly exhibits negligible dependence on the system-side harmonic current， the fluctuation level of the system-side harmonic current in the deviation formulation can be eliminated by using the covariance characteristic of random vectors， and the system-side harmonic impedance and the customer-side harmonic voltage emission level can be calculated. In addition， an influence factor that represents the influence degree of the fluctuation of the system-side harmonic is introduced based on the similarity principle of pattern recognition theory to yield a confidence reference of the estimation results. Based on the analysis results of laboratory simulation and field test cases， it proves that the proposed method is effective to eliminate the estimation error caused by the fluctuation of the system-side harmonic current.