A semiconductor device and a fabrication method thereof are provided. The semiconductor device includes a semiconductor structure, a dielectric layer, a metal-semiconductor compound film and a cover layer. The semiconductor structure has an upper surface and a lateral surface. The dielectric layer encloses the lateral surface of the semiconductor structure and exposes the upper surface of the semiconductor structure. The metal-semiconductor compound film is on the semiconductor structure, wherein the dielectric layer exposes a portion of a surface of the metal-semiconductor compound film. The cover layer encloses the portion of the surface of the metal-semiconductor compound film exposed by the dielectric layer, and exposes the dielectric layer.