The invention discloses an alignment mark for a GaN power device and a preparation method thereof, belonging to the field of semiconductor device processing. The alignment mark for the GaN power device comprises a primary metal alignment mark and a secondary metal alignment mark which are respectively positioned on a GaN substrate; the metal of the primary metal alignment mark is same as a drain-source metal of the GaN power device; and metal layers of the secondary metal alignment mark include a titanium layer, a platinum layer and a gold layer or the titanium layer, a molybdenum layer and the gold layer. The preparation method comprises the following steps of: (1) producing the primary metal alignment mark on the GaN substrate by using any one process before a high-temperature alloying process; (2) producing the secondary metal alignment mark on the GaN substrate by using the primary metal alignment mark; and (3) alloying the GaN substrate at high temperature of 800-1000 DEG C. By adopting the invention, the alignment precision of a non-contact grid photoetching process is improved, and thereby the direct current performance, the radio frequency performance and the reliability of the GaN power device can be improved.