The synchronization of the intelligent substation merging unit is directly related to the time consistency of the collected real-time data. The efficient merge unit synchronization calibration system ensures the data consistency of merging unit. This paper studies the reasons of the synchronization source and synchronization error of the merging unit, and discusses the common clock synchronization method. A merging unit calibration system based on phase shift method and frequency fine adjustment method is proposed, and the proportional integral regulator is introduced to synchronize the control system of the merging unit calibration system. It introduces the implementation process of PI-based merging unit synchronization calibration system. The actual test results show that the range of the synchronization deviation fluctuates from the original 600 ns to 900 ns interval to about 40 ns after using this method, which proves the effectiveness of the method. This work is supported by Science and Technology Project of State Grid Fujian Electric Power Company Ltd. (No. 521304150043).