In view of the difficulty of checking the changes of smart substation configuration files, this paper presents an online diagnosis method for smart substation configuration files based on double CRC checking. This method can effectively improve the security and consistency of smart substation configuration files. This method can efficiently realize the security and consistency of the configuration file. Firstly, the configuration file and its formation mechanism of smart substation based on IEC61850 are analyzed. Then it introduces the principle of CRC algorithm and its application in the dynamic check of the smart substation configuration file. It combines the characteristics of the substation configuration file with the principle of double decker CRC checking, and further studies the implementation process and specific steps of the method. Based on the double CRC checking method, an online diagnosis system for smart substation configuration files with visual functions is developed. The application of the on-line diagnosis system proves the effectiveness of the method. This work is supported by Science and Technology Project of Jiangxi Electric Power Company (No. 521820160015).