A substrate processing apparatus is disclosed. The substrate processing apparatus includes: a first process unit including a plurality of first process stations configured to perform a first process in a first atmosphere; a second process unit including a plurality of second process stations configured to perform a second process in a second atmosphere different from the first atmosphere; and a transformation unit between the first process unit and the second process unit. The first process unit, the transformation unit, and the second process unit are arranged in a line. The transformation unit includes a plurality of transformation stations configured to transform an atmosphere between the first atmosphere and the second atmosphere. Thus, the efficiency of processing a substrate can be improved, and the area or length in which the substrate processing apparatus is installed can be reduced.