Based on the theory of time-varying dynamic phasors， this paper finds that the currents fluctuation characteristic has an effect on the assessment accuracy of power system harmonic impedance using the fluctuation method， and that the relationship between the system harmonic impedance， harmonic voltage and harmonic current is non-linear at the common coupling point. In some cases， the assessment error of the system harmonic impedance based on the fluctuation method may be significant. Therefore， this paper proposes a least squares fitting algorithm to assess the magnitude of system harmonic impedance. Typical Monte Carlo simulations are carried out on PSCAD. Results show that the proposed method is valid and more suitable for engineering application.