There is provided a film forming position misalignment correction method comprising: replacing a shielding member; loading a substrate into a film forming module by a transfer mechanism and forming a film on the substrate; detecting an amount of film forming position misalignment by transferring the substrate on which the film has been formed to a film thickness measuring device; correcting a transfer position of the substrate for the transfer mechanism; and checking the correction by transferring the substrate used for measuring the amount of film forming position misalignment to the film forming module by the transfer mechanism for which the transfer position has been corrected to form a film and determining the amount of film forming position misalignment by measuring a film thickness of the formed film by the film thickness measuring device in the same manner.