The invention provides a method and system for cleaning a substrate with ultraviolet light. The method and system are used for effectively removing organic matters adhering to the surface of the substrate without damage to the substrate. The method for cleaning the substrate with the ultraviolet light comprises the steps that the substrate is divided into at least two areas, the residual amount of the organic matters of the areas on the substrate is detected, and the positions of the areas are determined; according to the residual amount of the organic matters of the areas, the ultraviolet light radiation quantity of cleaning each area is determined; and the substrate is cleaned according to the determined ultraviolet light radiation quantities of cleaning the areas and the positions of the areas.