A fault diagnosis system of a transformer substation intelligent protection device comprises an intelligent terminal, a merging unit, a protection device and a network analyzer, wherein the intelligent terminal is connected with transformer substation primary equipment, the merging unit is connected with transformer substation secondary equipment, the protection device is respectively connected with the intelligent terminal and the merging unit through optical fibers, and the network analyzer is respectively connected with the protection device through an optical fiber. Except that optical fiber links accessed to the intelligent terminal and the merging unit are arranged on the protection device, the fault diagnosis system is further provided with an optical fiber link specially connected with the network analyzer, and fault diagnosis and quick positioning on the protection device are achieved through the network analyzer provided with a built-in fault diagnosis module and a built-in fault positioning module according to the received protection device data communication situation.