The invention relates to an intelligent protection system for a secondary open circuit of a current transformer. The system comprises a CT (current transformer) secondary loop terminal board, wherein a CT loop terminal board relay switch is mounted on the CT secondary loop terminal board; the output side of the relay switch is connected with a collection module; the output of the collection module is connected with an A/D conversion module; the A/D conversion module is connected with a data judgment processing module; the data judgment processing module is provided with an output threshold value of the CT secondary loop terminal board; when a received signal is greater than the threshold value, the data judgment processing module sends out a trigger signal to a relay switch coil to enable the relay to be closed; and meanwhile, the data judgment processing module is connected with a data communication module and used for sending the received data to a background monitoring computer. By adoption of the intelligent protection system, when the CT secondary open circuit suffers from a high voltage, the CT secondary loop can be closed to eliminate the risk of burning down a winding by an overheated iron core so as to eliminate the threat from the secondary side high voltage.