Based on the analysis of technology source, technology function and application purpose in IEC 61850 substation secondary system, this paper discussed the commissioning work of substation and intelligent electronic device (IED) integration. According to the technical features and commissioning differences of secondary system and traditional system, this paper studied the target, difference and relation of configuration debugging and engineering commissioning for the secondary system. According to the content and purposes of the substation commissioning, the engineering commissioning method and quality control strategy of the secondary system were also constructively discussed combined with the structure and functional characteristics of the secondary system, especially the process integrity and overall quality control of the project commissioning.