The present disclosure provides a method of increasing the wafer throughput by an electron beam lithography system. The method includes scanning a wafer using the maximum scan slit width (MSSW) of the electron beam writer. By constraining the integrated circuit (IC) field size to allow the MSSW to cover a complete field, the MSSW is applied to decrease the scan lanes of a wafer and thereby increase the throughput. When scanning the wafer with the MSSW, the next scan lane data can be rearranged and loaded into a memory buffer. Thus, once one scan lane is finished, the next scan lane data in the memory buffer is read for scanning.