A method of joining semiconductor substrates includes: forming an alignment key on a first semiconductor substrate; forming a first protrusion and a second protrusion, and an alignment recess positioned between the first protrusion and the second protrusion on a second semiconductor substrate; forming a first metal layer and a second metal layer on the first protrusion and the second protrusion, respectively; and joining the first semiconductor substrate and the second semiconductor substrate, in which the alignment key is positioned at the alignment recess when the first semiconductor substrate and the second semiconductor substrate are joined.