To address the problem of heavy distributed debugging workload and communication failure of virtual terminal loop in intelligent substation secondary protection equipment, a cross-interval maintenance system based on SCD file and CCD file calibration is introduced. The system is mainly composed of consistency ratio and synchronous control detection. Based on the correct result of consistency comparison between the SCD file and the CCD file, this paper makes nine sets of power amplifiers output synchronously at most by using the theory of optical clock synchronization. Each power amplifier can output three phase voltage and three phase current and re-collect intelligent terminal protection tripping signals through hard contact of eight-way switch of power amplifier to realize one-time closed loop maintenance test of multi-spacing protection, for example main transformer, line, etc. Intelligent substation cross-interval maintenance system based on SCD file and CCD file calibration realizes multi-interval integral test of secondary equipment in intelligent substation, which has certain reference value for improving debugging and maintenance efficiency of intelligent substation and carrying out automatic test of the whole station. This work is supported by 2017 Science and Technology Project of Chongqing Electric Power Company “Research on Onsite Simulation Test Techniques in Smart Substation”.