The invention discloses a logical configuration method of a relay protecting device. The method comprises the steps of building a functional module library for the relay protecting device in a transformer substation; selecting a functional module element as requirement; performing configuration editing for a device interface signal and working logic through a module connecting line and according to the property configuration; examining the connection validity; processing a logic loop; fixing the calculation sequence of the configuration modules; generating a sequence which can be compiled and can perform operation; generating an executable mapping file. The method is applied to functional logical configuration of the relay protecting device in the transformer substation; the function of the relay protecting device in the transformer substation can be achieved through module configuration; the executable mapping file for the operation of the relay protecting device is generated; therefore, the logic generation efficiency of the device protecting/ measuring control device can be effectively increased, the device can be flexibly and easily updated while being used at the field, and moreover, the device operation can be monitored and maintained well; the technological means are provided for achieving intelligent device of the transformer substation, flexible application and function expanding.