A substrate cleaning apparatus capable of removing particles that exist in minute recesses formed on a substrate surface is disclosed. The substrate cleaning apparatus includes a substrate holder configured to hold a substrate; and a two-fluid nozzle configured to deliver a two-fluid jet onto a surface of the substrate. The two-fluid nozzle includes a first jet nozzle configured to emit a first two-fluid jet and a second jet nozzle configured to emit a second two-fluid jet at a velocity higher than a velocity of the first two-fluid jet, and the second jet nozzle surrounds the first jet nozzle.