The present disclosure provides a dithering method of increasing wafer throughput by an electron beam lithography system. The dithering method generates an edge map from a vertex map. The vertex map is generated from an integrated circuit design layout (such as an original pattern bitmap). A gray map (also referred to as a pattern gray map) is also generated from the integrated circuit design layout. By combining the edge map with the gray map, a modified integrated circuit design layout (modified pattern bitmap) is generated for use by the electron beam lithography system.