The invention relates to an automatic function compatibility identifying method on the basis of combined well-aligned feature codes and belongs to the technical field of automation of power system transformer substation. The automatic function compatibility identifying method includes creating the combined well-aligned feature codes in a device, setting up a relation table of the combined well-aligned feature codes and functional object interfaces of various service modules, looking up an function object most compatible with the combined well-aligned feature codes from the relation table according to the appointed combined well-aligned feature codes, binding the function object, and realizing compatibility of the various modules in the device. Under the condition that normal performance of the device is unaffected, abnormalities of the device due to functional compatibility of the various function modules of a relay protection device can be effectively reduced, reduction of maintenance cost of an embedded relay protection product is benefited and reliability and operation efficiency are improved.