A method of manufacturing a semiconductor device includes embedding electrodes in insulating layers exposed to the joint surfaces of a first substrate and a second substrate, subjecting the joint surfaces of the first substrate and the second substrate to chemical mechanical polishing, to form the electrodes into recesses recessed as compared to the insulating layer, laminating insulating films of a uniform thickness over the entire joint surfaces, forming an opening by etching in at least part of the insulating films covering the electrodes of the first substrate and the second substrate, causing the corresponding electrodes to face each other and joining the joint surfaces of the first substrate and the second substrate to each other, heating the first substrate and the second substrate joined to each other, causing the electrode material to expand and project through the openings, and joining the corresponding electrodes to each other.