The invention discloses an alignment method for a photoetching device. The alignment method is characterized by comprising the steps of 1, arranging an alignment mark on a silicon wafer; 2, irradiating the alignment mark by a lighting beam, wherein multi-stage secondary diffraction is performed on the alignment mark, and each stage secondary diffraction light passes through a 4F optical system and then forms an image on a detector arranged on an image surface of the 4F optical system; 3, respectively selecting a pixel point at a special position of each stage secondary diffraction imaging as a reference point of the each stage secondary diffraction imaging by a signal processing module when the alignment mark is in a static state; and 4, monitoring to obtain a light intensity curve, changing with the motion of the alignment mark, of the light intensity of the reference point of each stage secondary diffraction imaging by the signal processing module when the alignment mark is in a moving state, and completing alignment when the light intensity of the reference point of each stage secondary diffraction imaging is simultaneously peak value. The invention also discloses an alignment system for implementing the alignment method for the photoetching device.