A method for fabricating a high voltage semiconductor device is provided. Firstly, a substrate is provided, wherein the substrate has a first active zone and a second active zone. Then, a first ion implantation process is performed to dope the substrate by a first mask layer, thereby forming a first-polarity doped region at the two ends of the first active zone and a periphery of the second active zone. After the first mask layer is removed, a second ion implantation process is performed to dope the substrate by a second mask layer, thereby forming a second-polarity doped region at the two ends of the second active zone and a periphery of the first active zone. After the second mask layer is removed, a first gate conductor structure and a second gate conductor structure are formed over the middle segments of the first active zone and the second active zone, respectively.