A substrate processing apparatus includes a plurality of cells each including a predetermined processing unit, a transport mechanism, and a cell controller. The cell controller independently controls operations in each cell in accordance with transport setting and processing condition setting for each cell described in recipe data determined for each substrate unit to be processed. Because the processing and transport are performed independently of the operations of adjacent cells, substrates belonging to different substrate units are received through a feed inlet or the same substrate inlet, are processed while being present in the same cell, and are transported to a feed outlet and a return outlet which are different substrate outlets. This allows the presence of different process flows in parallel.