Disclosed are methods of manufacturing a semiconductor device. The method of manufacturing one semiconductor device includes forming a transistor structure on a semiconductor substrate, forming a metal interconnection layer on the transistor structure, forming a protective layer on the metal interconnection layer, and implanting hydrogen ions into the semiconductor substrate having the protective layer by using a hydrogen ion implanter. Hydrogen ions are stably and effectively implanted into a selected region by using a hydrogen ion implanter in the manufacturing process of the semiconductor device, thereby facilitating the manufacturing process and improving the performance of the semiconductor device.