This paper proposes a new method to estimate system harmonic impedance and harmonic emission level based on the pan-normal impedance cloud. First of all, based on the basic principle of fluctuation method, it can be obtained that the key to estimate the system harmonic impedance is how to identify fluctuation ratio samples closer to the true value through theoretical analysis; Secondly, through studying the probability distribution of fluctuation ratio, this paper finds that the pan-normal distribution characteristic of fluctuation ratio meets the applicable conditions of normal cloud model so that the digital features of impedance cloud can be calculated by backward cloud generator; Finally, based on the “3En" Rules” of cloud model, the filtering threshold of impedance can be obtained, then the system harmonic impedance and harmonic emission level can be estimated by filtering qualified samples. Through the simulation of theoretical model and calculation of practical engineering examples, it proves the accuracy and effectiveness of the proposed method.