As the main information source of intelligent substation, electronic transformer needs to be checked regularly, and ensuring time synchronization is the most critical link in the process of transformer calibration. Based on the previously designed real-time collaborative monitoring system for CT side cloud, this paper constructs a multi-CT side cloud collaborative measurement system. Both standard CT and verified CT are integrated with the monitoring system to form a CT side cloud collaborative measurement unit. Each measurement unit transmits the data collected by CT remotely in real time to the cloud storage, then uniformly exported to the edge computing side for CT verification calculation. Theoretical clock errors and link delay errors of data uploading to the cloud between each measurement unit are analyzed, and a master/ slave clock error model of CT calibration is established. A master/ slave clock error correction algorithm based on KF and RBF-PID is proposed for CT calibration to ensure time synchronization during CT calibration. The proposed algorithm is verified by simulation. Under different initial conditions, the corrected errors of master and slave clocks are all less than 200 ns, and the convergence time is about 0. 4 s. Finally, the feasibility and practicability of the proposed algorithm are verified by experiments. The calibration results of the CT corrected by the error of the master and slave clock are more accurate, with the phase error of about 0. 45″ and the amplitude error of about 0. 003 58%, meeting the requirement of 0. 1 accuracy level.