The invention provides a method for configuring a protection device of a generator-transformer unit. The method comprises the following steps of: configuring a system parameter, configuring a channel, configuring a relay and making a wiring diagram, wherein the step of configuring the system parameter comprises configuring a generator parameter, a main transformer parameter, a high voltage service transformer parameter, an excitation transformer parameter, a branch cable parameter, a spare transformer parameter, a generator-transformer unit differential parameter, and the quantity of an inletplug-in unit, a signal plug-in unit and an outlet plug-in unit; the step of configuring the channel comprises configuring an analog channel, an inlet channel, an outlet channel, and signal channel; the step of configuring the relay comprises, according to the system configuration, automatically generating a relative relay list and configuring the analog channel relevant to each starting relay, the inlet channel relevant to each starting relay and the signal channel relevant to each starting relay; and the step of making the wiring diagram comprises automatically generating the wiring diagram according to the system configuration and associating each relative exchange channel of each diagram resource with a corresponding analog channel.