A substrate processing apparatus configured to process a substrate, the substrate processing apparatus including: a processing chamber; and a support structure located in the processing chamber and having a tray supporting surface for supporting a tray on an upper surface of the support structure, wherein the tray is formed with a recess accommodating the substrate on an upper surface of the tray, the support structure includes a lift pin to lift and lower the tray at an upper portion of the support structure, the support structure has a through-hole into which the lift pin is inserted, and the through-hole is at a position where the through-hole does not overlap with the tray in plan view when the tray is located on the support structure.