A method for measuring critical dimensions of a pattern using an overlay measuring apparatus is provided. The method includes setting a first scan range, inputting a step pitch for the overlay measuring apparatus, inputting X and Y coordinates of a point on a reticle, and inputting a size of the reference pattern. The method further includes inputting a position of the reference pattern, inputting a second scan range, measuring the size of the reference pattern, and inputting an ideal pattern size. The method still further includes measuring a size and a first Z-axial focus position of a top region of the reference pattern, storing the first Z-axial focus position, measuring a size of the selected pattern of the first wafer using stored reference information, and determining whether the size of the selected pattern is suitable relative to the ideal pattern size.