An alignment unit includes a measurement unit configured to measure a coordinate of a center position of an alignment mark transferred to each layer that is located under an uppermost layer of a substrate, and a controller configured to determine a target coordinate of the center position of the alignment mark transferred to the uppermost layer of the substrate based on a result of a weighted average that is made by weighting the coordinate of the center position of the alignment mark of each layer of the substrate measured by the measurement unit using as a weight a function inversely proportional to a minimum critical dimension of the pattern of an original formed on each layer of the substrate.