The present invention is related with a method of cleaning a substrate by ultraviolet rays with adjustable radiation energy, comprising steps of: providing an ultraviolet ray light (10) and a substrate (20) to be cleaned with the ultraviolet rays; locating several shading plates (30) between the ultraviolet ray light (10) and the substrate (20) to be cleaned with the ultraviolet rays; rotating the shading plates (30) to adjust an area of the substrate (20) irradiated with the ultraviolet rays emitted by the ultraviolet ray light (10) and thus to control the radiation energy on the substrate (20) in the unit time; cleaning the substrate (20) with the ultraviolet rays emitted by the ultraviolet ray light (10). With the method, the radiation energy of the ultraviolet rays for cleaning the substrate can be flexibly adjusted. The objectives of efficiently removing the organic matter stick on the surface of the substrate and preventing the static damage to the circuit pattern of the substrate can be achieved. Thus, the quality and the yield of the productions can be promoted.