A method of correcting an overlay error includes the following steps. First, an overlay mark disposed on a substrate is captured so as to generate overlay mark information. The overlay mark includes at least a pair of first mark patterns and at least a second mark pattern above the first mark patterns. Then, the overlay mark information is calculated to generate an offset value between two first mark patterns and to generate a shift value between the second mark pattern and one of the first mark patterns. Finally, the offset value is used to compensate the shift value so as to generate an amended shift value.