A pattern inspection apparatus includes a sample including a plurality of holes having thicknesses that are different from each other, an electron gun configured to generate an input electron beam and emit the input electron beam onto a wafer and the sample, a stage configured to support the wafer and the sample, a detector configured to generate a scanning electron microscope (SEM) image by detecting emitted electrons from the wafer and the sample, and a processor configured to process the SEM image into a three-dimensional profiling image containing depth information of the wafer and determine whether a condition of the input electron beam has changed based on the processing of the SEM image.