A method of manufacturing a semiconductor device includes forming an opening in a first substrate and filling the opening with a metal to form a first connection electrode. The first substrate is then polished by chemical mechanical polishing under conditions such that a polishing rate of the metal is less that of the region surrounding the metal. The chemical mechanical polishing thereby causes the first connection electrode to protrude from the surface of the first substrate. The first substrate is stacked with a second substrate having a second connection electrode. The first and second connection electrodes are bonded by applying pressure and heating to a temperature that is below the melting point of the metal of the first connection electrode.