A manufacturing method of a glass substrate having holes includes irradiating a plurality of hole formation target positions of a dummy glass substrate with a laser under a first condition, to form a plurality of holes in the dummy glass substrate; heating the dummy glass substrate under a second condition; measuring, for each of the hole formation target positions, a deviation between the hole formation target position and a position of the hole after the heating formed by irradiating the hole formation target position of the dummy glass substrate; irradiating irradiation target positions of a glass substrate, having substantially same shape, dimension and composition as the dummy glass substrate, with a laser under the first condition, to form a plurality of holes, the irradiation target positions of the glass substrate with the laser being determined taking into account the deviation; and heating the glass substrate under the second condition.