Provided are a method of evaluating an ion irradiation effect, a process simulator and a device simulator, which allow the influence of ion irradiation on atoms making up a substrate to be evaluated with high accuracy. The method includes irradiating a sample with a beam of ions, and evaluating influence of the ions used for the irradiation on atoms making up the sample, provided that the sample is prepared by alternately and periodically stacking a plurality of thin film layers, and of the plurality of thin film layers, the layer of at least one kind is composed of an isotope layer.