According to the five basic elements of production workshop, product, output, technological process, auxiliary department, and time, the layout design optimization of ship cutting and machining center is conducted with the Systematic Layout Planning （SLP） method. Taking the logistics and non-logistics factors, integrated relationship, position and area into comprehensive consideration, the virtual simulation technology is applied to comparatively analyze the layout design schemes, and it is verified that the layout design optimization scheme with the SLP method is beneficial to improving the station production efficiency, reducing the invalid time percentage, then achieving the lean production.