A substrate cleaning apparatus includes: a substrate holder configured to hold and rotate a substrate; an ultrasonic cleaning unit configured to impart an ultrasonic vibration energy to deaerated pure water and then supply the deaerated pure water onto a surface of the substrate; a pure water spray nozzle configured to spray deaerated pure water onto the surface of the substrate; a chamber surrounding the substrate holder and the pure water spray nozzle; and an inert gas supply line configured to supply an inert gas into the chamber.