Provided is a substrate processing apparatus including: a carry-in area where a placing table is provided to place thereon a carrying container including a take-out opening, a flange formed on an upper portion of a side formed with the take-out opening, and a recess formed on a top surface of the flange; a transfer area maintained under an atmosphere different from that of the carry-in area; a partition wall configured to partition the carry-in area and the transfer area and formed with an opening; a door configured to open/close the opening; a carrying container pressing unit configured to press the carrying container placed on the placing table against the partition wall so that the take-out opening of the carrying container faces the opening of the partition wall; and a carrying container holding unit configured to be inserted into the recess to press the carrying container against the partition wall.