The small-signal stability assessment of three-phase systems can be performed using the measured impedances of the load and source. To obtain the dc steady-state 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 measurements. This paper investigates the impact of synchronization dynamics on the accuracy of the measured impedance. It is revealed that the synchronization dynamic in the perturbation injection has little effect on the measured impedance, while the synchronization dynamic introduced in the impedance calculation can have significant effect. Based on the relationship between voltage and current in the measured dq-frame and in the actual dq-frame, an improved impedance calculation method is developed. The method can reduce the errors caused by the phase dynamics considering both the injected perturbations and system frequency variations. Finally, simulations and experimental results verify the accuracy of the theoretical analysis and the effectiveness of the method.