The invention relates to a station-domain protection system of an intelligent transformer station and a function debugging method of the system. A station-domain protector is mounted between an integrated application server and monitor host and a central switch of a process layer, the station-domain protector is networked with the integrated application server and monitor host via MMS messages, and the integrated application server and monitor host is networked with the central switch of the process layer via GOOSE and SV messages. The debugging technology as well as single debugging, network debugging and group transmission methods of station-domain protection of the new generation of intelligent transformer station are included, the workload of equipment maintenance is reduced, wire arrangement is greatly reduced, wiring is simple and convenient, the installation efficiency is effectively improved, the whole construction period is shortened, and the operation stability of the system is improved.