A semiconductor device includes: a semiconductor substrate; a semiconductor layer disposed over the semiconductor layer; a first well region disposed in the semiconductor layer and the semiconductor substrate; a second well region disposed in the semiconductor layer; a first isolation element disposed in the first well region; a second isolation element disposed in the second well region; a gate structure disposed in the semiconductor layer between the first isolation element and the second isolation element; a first doped region disposed in the first well region; and a second doped region disposed in the second well region. The bottom surface of the gate structure is above, below or substantially level with a bottom surface of the first isolation structure.