A high voltage metal-oxide-semiconductor transistor device having stepped gate structure and a manufacturing method thereof are provided. The manufacturing method includes following steps. A gate structure is formed on a semiconductor substrate. The semiconductor substrate includes a first region and a second region disposed on a side of a first part of the gate structure and a side of a second part of the gate structure respectively. A patterned mask layer is formed on the semiconductor substrate and the gate structure. The patterned mask layer covers the first region and the first part. The second part is uncovered by the patterned mask layer. An implantation process is performed to form a drift region in the second region. An etching process is performed to remove a part of the second part uncovered by the patterned mask layer. A thickness of the second part is less than that of the first part after the etching process.