An object of the invention is to effectively remove particles on the glass substrate surfaces, even in the case wherein abrasive particles having a small particle size is used in the polishing step of the glass substrate and a supersonic treatment is performed at a high frequency at the supersonic cleaning step after the polishing step. In a manufacturing method of a glass substrate for a magnetic disk comprising a polishing step for performing polishing of the glass substrate and a supersonic cleaning step for performing supersonic cleaning of the glass substrate after the polishing step, the polishing step uses abrasive particles having a particle size of 10 nm to 30 nm and a first supersonic cleaning is performed at a frequency of 300 kHz to 1,000 kHz to form secondary particles and then a second supersonic cleaning is performed at a frequency of 30 kHz to 100 kHz in the supersonic cleaning step.