A transistor device and a manufacturing method thereof are provided. The transistor device includes a substrate, a first well, a second well, a shallow trench isolation (STI), a source, a drain and a gate. The first well is disposed in the substrate. The second well is disposed in the substrate. The STI is disposed in the second well. The STI has at least one floating diffusion island. The source is disposed in the first well. The drain is disposed in the second well. The electric type of the floating diffusion island is different from or the same with that of the drain. The gate is disposed above the first well and the second well, and partially overlaps the first well and the second well.