A drill holding tool includes a shaft and a drill-holding portion which has a recess defined axially in an outer periphery thereof so as to receive a flat center drill therein which has one end protrudes out from the distal end of the drill-holding portion. The recess is defined by two sidewalls and a bottom surface, and a threaded hole is defined through the bottom surface. Two semi-circular reception holes are defined in two insides of the two sidewalls and two positioning pieces are received in the reception holes. The center drill includes a positioning hole corresponding to the threaded hole in the recess and two semi-circular positioning notches in which the two positioning pieces are partially received. The center drill is a flat piece which saves material required and the positioning notches allow the center drill to be quickly and precisely positioned.