During the process of the intelligent substation construction, reconstruction, expansion and daily operation and maintenance, Substation Configuration Description (SCD) files need to be modified frequently, which makes version management difficult. For this purpose, the control system of SCD file is designed and developed. The system ensures the minimum scope of SCD file modification through the decoupling technology of relevant intervals. By using SVN management technology to control the version of SCD document effectively, the correctness and traceability of the configuration information in the entire life cycle of the substation can be guaranteed. Via visualization technology, the modification of SCD file content is visually displayed to the user, which reduces the technical requirements for using personnel. Several pilot projects indicate that the system fully meets the requirements for SCD file version control in different stages and can effectively improve the security and implementation efficiency of SCD file upgrade and modification. This work is supported by Science and Technology Project of China Southern Power Grid Company:Key Techniques Research and Application for Intelligent Substation Homologous Maintenance (No. GD-KJXM-20162131).