1. A method for aligning wafer, comprising the steps of: (a) loading and aligning a first wafer in an exposure apparatus; (b) selecting a non-defective wafer alignment mark among a plurality of wafer alignment marks of the first wafer and storing the non-defective wafer alignment marks as a gray level reference image in a job file; (c) loading a second wafer and storing a plurality of wafer alignment marks of the second wafer as a plurality of gray level wafer alignment mark images; (d) respectively comparing each of the plurality of wafer alignment mark images of the second wafer with the reference image of the first wafer pixel by pixel to obtain matching value for each of the plurality of the wafer alignment mark images; (e) comparing each of the plurality of the matching values with a minimum value set in the exposure apparatus; (f) replacing the wafer alignment mark image having the matching value smaller than the minimum value with the reference image; and (g) obtaining an alignment information for an underlying layer using a wafer alignment sensor.