The invention discloses a hydrogenation catalyst composition and a preparation method thereof. The hydrogenation catalyst composition comprises an aluminum oxide carrier, an active metal and an auxiliary agent, wherein the active metal is selected from one or more of VIII family and/or VIB family metallic elements, and the auxiliary agent is selected from one or two of silicon or zirconium; the concentration of silicon and/or zirconium in the catalyst, in the form of oxides, are gradually increased from centers to outer surfaces of catalyst particles, wherein the concentration of silicon and/or zirconium at a position of 1/3R of particles is 0.1-0.5wt%, the concentration of silicon and/or zirconium at a position of 2/3R is 0.5-1.0wt%, the concentration of silicon and/or zirconium at a position of R is 1.0-3.0wt%, and R is the semi-diameter of the catalyst particles by taking the center of the catalyst as an initial point. The catalyst prepared by adopting an impinging stream co-precipitation gel forming mode in the invention is centralized in particle size distribution, and has an ideal pore structure, and the auxiliary agent and the active metal are distributed in the catalyst in a gradient increase mode, so that the deactivation rate of the catalyst can be effectively reduced, and the desulfurization and denitrification capacities of the catalyst are improved.