Provided are a substrate cleaning apparatus and method and a brush assembly used therein. The substrate cleaning apparatus for contact-cleaning a substrate includes a cleaning brush rotatably disposed in a cylindrical shape and having an outer circumferential surface contacting the substrate to clean the substrate. Here, the cleaning brush includes a plurality of pressure chambers expanding by a fluid pressure and disposed along a longitudinal direction of a rotation axis rotating at a central portion of the cleaning brush, and the plurality of pressure chambers are individually expandable to allow a portion of the outer circumferential surface to protrude in a radial direction and thus contact-clean a portion of the substrate.