The Thevenin equivalent impedance online calculation can be applied to system stability analysis and online tuning of relay protection. The method based on hierarchical estimation is suggested after two types of Thevenin equivalent impedance calculation method principles and error causes have been analyzed. The proposed method's foundation and steps are presented, and an error analysis reveals that it stratifies the samples in accordance with the parameters on the load side and builds the calculation formulas in a way that can increase calculation accuracy and successfully counteract the fluctuating effects of the system's Thevenin equivalent impedance. The example analysis demonstrates that, with varied amplitude disturbances of the equivalent potential, the proposed method can identify the Thevenin equivalent parameters with fewer sampling numbers. Also it greatly minimizes the error compared to the two current methods. It can still estimate the Thevenin equivalent impedance even when the Thevenin equivalent impedance disturbance is included.