A lithography apparatus includes: a stage configured to hold the substrate; a scope configured to measure a position of a mark formed on a surface of the substrate; and a controller configured to control movement of the stage to form the pattern based on the position of the mark. When there is a rotation shift of the surface of the substrate about a first axis of one of X-, Y-, and Z-axes with respect to the stage, the controller estimates the position of the mark in a direction of a second axis perpendicular to the first axis based on an amount of the rotation shift, moves the stage in the direction of the second axis based on the estimated position of the mark, and then measures the position of the mark by the scope.