The present invention relates to a semiconductor device with a plurality of mark through substrate vias, comprising a semiconductor substrate, a plurality of original through substrate vias and a plurality of mark through substrate vias. The original through substrate vias and the mark through substrate vias are disposed in the semiconductor substrate and protrude from the backside surface of the semiconductor substrate. The mark through substrate vias are added at a specific position and/or in a specific pattern and serve as a fiducial mark, which facilitates identifying to the position and direction on the backside surface. Thus, the redistribution layer (RDL) or the special equipment for achieving the backside alignment (BSA) is not necessary.