An overlay operation method and an overlay control method are disclosed. A first mark and a second mark are identified on a substrate, wherein the first mark and the second mark are formed by a process in combination with using a photomask. Next, a first measurement is performed to obtain an offset between the first mark and the second mark in a direction. Then, an operation is performed to judge whether the offset is in a range from a pre-determined offset minus a deviation to the pre-determined offset plus the deviation, wherein the pre-determined offset is determined by the photomask.