An etching stopper film is formed on an interlayer insulating film. A conductive layer is formed on the etching stopper film. An etching stopper film is formed to cover the conductive layer. An interlayer insulating film is formed on the etching stopper film. In a structure above, initially, a hole vertically penetrating the interlayer insulating film for exposing a surface of the etching stopper film is formed under a first etching condition. Thereafter, the etching stopper film serving as a bottom surface of the hole is removed under a second etching condition, thereby forming the hole reaching the conductive layer. An interconnection is embedded in the hole. A semiconductor device in which a hole reaching the conductive layer is prevented from extending as far as the lower interlayer insulating film as a result of misalignment, as well as a manufacturing method thereof are thus obtained.