An exposure apparatus according to an embodiment controls the positioning between layers using an alignment correction value calculated on the basis of lower layer position information of a lower-layer-side pattern and upper layer position information of an upper-layer-side pattern. The lower layer position information includes alignment data, a focus map, and a correction value which is set on the basis of the previous substrate. The upper layer position information includes alignment data, a focus map, and a correction value which is a correction value for the positioning and is used when the upper-layer-side pattern is transferred.