A method of manufacturing a semiconductor device, wherein a first substrate where first electrode pads are formed and a second substrate where second electrode pads are formed are stacked and the first electrode pads and the corresponding second electrode pads are electrically connected thereby forming the semiconductor device is disclosed. The method includes steps of performing a first hydrophilic treatment with respect to the first electrode pads; supplying liquid to a surface where the first electrode pads are formed in the first substrate; and placing the second substrate on the first substrate to which the liquid is supplied so that the surface where the first electrode pads are formed opposes a surface where the second electrode pads are formed, thereby aligning the first electrode pads and the second electrode pads by the liquid that gathers in the first electrode pads that have been subject to the first hydrophilic treatment.