A semiconductor device and a manufacturing method thereof are disclosed. The method comprises: providing a substrate with a first dielectric layer and a gate, wherein the gate is embedded in the first dielectric layer and an upper portion of the gate is an exposed first metal; and covering only the exposed first metal with a conductive material that is harder to be oxidized than the first metal by a selective deposition. An advantage of the present invention is that the metal of the upper surface of the gate is prevented from being oxidized by covering the metal gate with the conductive material that is relatively harder to be oxidized, thereby facilitating the formation of an effective electrical connection to the gate.