Disclosed herein are a method and apparatus for scanning a multilayer material using magnetism. The apparatus for scanning a multilayer material includes at least one measurement head for exciting a mixed magnetic field on a multilayer specimen using at least one excitation solenoid coil and detecting detection signals from the multilayer specimen using a detection solenoid coil, a movement controller for moving any one of the at least one measurement head and a stage on which the multilayer specimen is placed in order to detect detection signals for all parts of the multilayer specimen, and a signal controller for generating two excitation signals having different frequencies in order to generate the mixed magnetic field and for generating a scanning result for the multilayer specimen by collecting the detection signals.