A substrate analysis system includes a load-lock module configured to load or unload a substrate on which a pattern layer is formed; a milling module configured to form a milling surface from which at least a portion of the pattern layer is removed; a depth measuring module configured to measure a milling depth of an analysis region formed on the milling surface; an imaging module configured to capture a two-dimensional image of the analysis region; and a control module controlling the substrate to circulate through the milling module, the depth measuring module, and the imaging module, when the milling depth is shallower than a set target depth, wherein the milling module adjusts a path of the ion beam so that the ion beam moves horizontally in the milling region according to a scanning profile received based on an intensity map of the ion beam.