A method for aligning an inhomogeneous receiver with an anisotropic emitter on a wafer probing system, wherein a reference semiconductor die comprising a reference pad and an anisotropic emitter is formed on a semiconductor wafer, the reference pad is located at a reference-pad-and-anisotropic-emitter relative position corresponding to the anisotropic emitter, the method comprises following steps of: measuring a receiver center position of an inhomogeneous receiver configured on a wafer probing system by a profile sensor; measuring a reference tip position of a reference tip of a reference probe on a probe card by a measuring instrument; displacing the inhomogeneous receiver in an aligning displacement according to the reference-pad-and-anisotropic-emitter relative position, the reference tip position and the receiver center position; and aligning the reference tip with the reference pad by a probe-tip-and-pad aligning machine of the wafer probing system.