An exposure apparatus for transferring a pattern of a reticle onto a wafer is provided. The exposure apparatus includes an illumination module, a reticle stage, a projection module, a wafer stage, and a control unit. The control unit is configured to calculate an alignment setting of the reticle. The wafer includes a first layer and a second layer disposed on the first layer. The first layer includes a first alignment parameter. The second layer includes a second alignment parameter. The control unit obtains a first weighting factor predetermined according to a property of the first layer, and a second weighting factor predetermined according to a property of the second layer. The alignment setting of the reticle is calculated according to the first alignment parameter, the first weighting factor, the second alignment parameter, and the second weighting factor.