Provided are an apparatus and a method of cleaning a substrate. The apparatus includes a substrate supporting unit supporting a substrate, a container surrounding the substrate supporting unit and collecting an organic solvent scattered from the substrate, and a fluid supplying unit provided on one side of the container and spraying a liquid organic solvent with bubbles to the substrate. The fluid supplying unit includes a nozzle head ejecting the organic solvent to the substrate, an organic solvent supplying line supplying the organic solvent from an organic solvent storage tank to the nozzle head, and a bubble providing element provided on the organic solvent supplying line and providing bubbles to the liquid organic solvent.