A method of manufacturing a through-hole electrode substrate includes forming a plurality of through-holes in a substrate, forming a plurality of through-hole electrodes by filling a conductive material into the plurality of through-holes, forming a first insulation layer on one surface of the substrate, forming a plurality of first openings which expose the plurality of through-hole electrodes corresponding to each of the plurality of through-hole electrodes, on the first insulation layer and correcting a position of the plurality of first openings using the relationship between a misalignment amount of a measured distance value of an open position of a leaning through-hole among the plurality of through-holes and of a design distance value of the open position of the leaning through-hole among the plurality of through-holes with respect to a center position of the substrate.