A motor controller for an electronic driving motor, including at least a controlling and processing unit, an interface circuit unit, and an identifying circuit. The controlling and processing unit is disposed on a mother circuit board. The interface circuit unit and the identifying circuit are disposed on a daughter circuit board. The mother circuit board and the daughter circuit board are connected to each other whereby forming electric connection. The identifying circuit inputs an identifying signal to the controlling and processing unit. The controlling and processing unit automatically configured types of input/output ports of the interface circuit unit according to the identifying signal. The motor controller of the invention enables motor manufactures to reduce the number of motor types for management, reduces development cost, development cycle, and product cost, simplifies a production technique, and improves efficiency.