There is provided a glass substrate manufacturing method for manufacturing a glass substrate with a plurality of through-holes. The method includes a laser processing of forming the plurality of through-holes in the glass substrate, the glass substrate having a first main surface and a second main surface facing the first main surface, by irradiating a laser beam toward the first main surface; and an etching process of injecting an etchant only from a position facing the second main surface of the glass substrate toward the plurality of through-holes formed in the glass substrate.