The invention provides a hydrogenation catalyst and a preparation method and application thereof. The preparation method comprises the steps of: firstly loading a shaped carrier with active metal nickel to obtain a carrier S1, then load the carrier S1 with a phosphorus source to obtain a carrier S2, and then activating the carrier S2 under a hydrogen atmosphere to obtain the hydrogenation catalystcontaining metal phosphide NixPy, wherein the ratio of x to y is (1:3)-(1:7), the carrier accounts for 60-80% of the total weight of the hydrogenation catalyst, and the molar ratio of nickel atoms tophosphorus atoms which are used for preferable selection of the loaded active metal nickel and phosphorus source is (1:3)-(1:7). The hydrogenation catalyst is suitable for hydrodesulfurization and hydrodenitrogenation reactions of diesel oil under mild conditions, and the hydrogenation catalyst has the main advantage of high selectivity to direct desulfurization and/or denitrification during thereactions.