An imprint apparatus that performs an imprint process of forming a pattern on a shot region of a substrate using a mold is provided. The apparatus comprises a mold holder for holding the mold, and a deformation mechanism for deforming a pattern region of the mold held by the mold holder. Based on a response property of the mold when the force is applied to the mold by the deformation mechanism, a setting load is applied to the mold by the deformation mechanism before the mold and the imprint material are brought into contact with each other, and the pattern region of the mold is deformed by the deformation mechanism, after the mold and the imprint material have been brought into contact with each other, so as to reduce an overlay error between the shot region and the pattern region.