Abstract: A grading system and an application of a hydrogenation catalyst and a grading method of the hydrogenation catalyst are provided. The system contains M hydrogenation catalysts sequentially filled in a material flow direction. An R value of an Nth hydrogenation catalyst is not less than an R value of an (N?1)th hydrogenation catalyst, and the R value of at least one Nth hydrogenation catalyst is greater than the R value of the (N?1)th hydrogenation catalyst. N is an integer greater than 2 and not greater than M; the R value is a ratio of molar content of the VIII group metal element in the hydrogenation catalyst characterized by an X-ray photoelectron spectrum to weight content of the VIII group metal element in terms of oxides in the hydrogenation catalyst characterized by an X-ray fluorescence spectrum. The hydrogenation catalysts having different surface nickel atom concentrations are used for grading, thereby improving denitrification and the hydrogenation saturation performance of a catalyst system.