The invention provides a hydrogenation catalyst and a preparation method and application thereof. The preparation method of the catalyst comprises the following steps of: loading active metal nickel on a shaped carrier to obtain a carrier S-1, then loading a phosphorus source to obtain a carrier S-2, and then activating the carrier S-2 under the atmosphere of hydrogen to obtain the hydrogenation catalyst containing metal phosphide NixPy, wherein the ratio of x to y is (1:3)-(1:7), and the carriers account for 60-80% of the total weight of the hydrogenation catalyst. The catalyst is suitable for hydrodesulfurization and hydrodenitrogenation reactions of diesel fuel under mild conditions, and has the main characteristic that the catalyst has high selectivity to direct desulfurization and/ordenitrification during the reaction process.