Small-signal stability assessment of the threephase system can be performed using the measured impedances of the load and source. To obtain the dc steadystate operation point, the impedances are measured in the rotating dq-frame, and the phase angle is needed for the coordinate transformation used in both the perturbation injection and the impedance calculation. However, the phase estimation may introduce additional dynamics, affecting the accuracy of impedance measurement. This paper investigates the impact of phase synchronization dynamics on the measured impedance results. It is revealed that the phase variations in the perturbation injection has little effect on the measured impedance, while the phase dynamics introduced in the impedance calculation may have a significant impact. Based on impedance transformation, a new impedance calculation method is proposed, which can reduce the errors caused by the phase dynamics. Finally, the simulation and experiment results verify the accuracy of the analytical results and the effectiveness of the proposed method.