According to an aspect of the invention, there is provided a substrate cleaning method of discharging cleaning liquid from a nozzle above a processing target substrate to clean the substrate while rotating the substrate such that the nozzle is scanned from the center of the substrate toward an outside of the substrate while discharging the cleaning liquid from the nozzle toward the substrate to scatter the cleaning liquid toward the outside of the substrate, comprising controlling a flow rate of the cleaning liquid, a rotational speed of the substrate, a scan speed of the nozzle, and a scan start position of the nozzle such that the cleaning liquid discharged from the nozzle does not impinge on the old cleaning liquid remaining on the substrate when the cleaning liquid discharged from the nozzle contacts a surface of the substrate.