To calculate the harmonic impedance on the system side is crucial for the safe and stable operation of the new power system. Existing algorithms for harmonic impedance estimation usually assume that the harmonic impedance on the system side is constant during the measurement period. However, the voltage on the system side always changes according to the working mode of the power grid or access of large power load demand, resulting in fluctuations of the harmonic impedance on the system side. Luckly, the harmonic impedance on the system side does not change much in the adjacent sampling time interval. On this basis, the paper proposes a new non-intervention solution for the variable harmonic impedance on the system side. In this method, the second-order change of the harmonic impedance and the second-order change of voltage in the adjacent sampling time interval are taken as the objective function. The harmonic impedance on the system side is solved by minimizing the target function. The proposed method is proved to be accurate and reliable by simulation and practical analysis, especially in the condition that the strong background harmonic or user-side harmonic impedance is not much stronger than the harmonic impedance on the system side.