In one embodiment, a substrate processing control apparatus includes a position information acquiring module configured to acquire information about a position of a first pattern that is formed in a substrate for a photomask to change an applied stress to the substrate or a transmittance of the substrate. The apparatus further includes a position determining module configured to determine, in accordance with the information about the position of the first pattern, a position of a second pattern to be formed in the substrate to change the applied stress to the substrate or the transmittance of the substrate.