Abstract: In the transformation of smart grids, the secondary electrical system plays a core role in grid monitoring and protection, with merging units being key components that connect primary equipment to secondary protection devices. The sampling synchronization performance of merging units directly affects relay protection accuracy. This paper addresses the impact of sampling synchronization deviation on protection reliability, analyzing the deviation mechanism and its effects on differential and distance protection. A multi-level calibration strategy combining hardware clock calibration, software dynamic compensation, and system-level verification is proposed. The results show that this strategy effectively suppresses deviations, reducing differential errors by 96.8% and limiting impedance angle errors within 0.04° under a 50μs deviation. This study provides a systematic solution for improving protection accuracy.