A wafer alignment system is provided for performing a unidirectional scan-exposure. The wafer alignment system includes a plurality of wafer stages successively moving from a first position to a second position of a base cyclically. The wafer alignment method also includes an encoder plate having a first opening and a second opening. Further, the wafer alignment system includes a plurality of encoder plate readers and a plurality of wafer stage fiducials on the wafer stages. Further, the wafer alignment system also includes an alignment detection unit above the first opening of the encoder plate.