A method of manufacturing a semiconductor device, includes: forming a first circuit substrate having a first interconnection; forming a second circuit substrate having a second interconnection; bonding the first circuit substrate to the top surface of the second circuit substrate so as to be stacked facing each other; and performing an etching process of simultaneously removing parts formed on the first interconnection and the second interconnection in a stacked body of the first circuit substrate and the second circuit substrate so as to form a first opening in the top surface of the first interconnection and to form a second opening in the top surface of the second interconnection. The forming of the first circuit substrate includes forming an etching stopper layer on the surface of the first interconnection out of a material having an etching rate lower than that of the first interconnection in the etching process.