The invention provides a method for marking a wafer, which comprises providing a wafer having at least two reference marks, wherein a surface of the wafer comprises a plurality of crystal grains, at the same time, detecting the reference marks of the wafer to perform a wafer alignment, and marking the wafer by a laser. In addition, the invention can be suitable for marking the crystal grains of the wafer (for example, throwout crystal grains), comparing to the prior art of marking the throwout crystal grains by ink, has advantages of less wafer pollution, operation time, workshop space and permanent marker, is easier to reconstruct by the existing wafer tester or ink machine platform.