The invention discloses a preparation method of a hydrofining catalyst. The method comprises the following steps of in the presence of an organic compound, preparing nickel and aluminum precipitates by a normal precipitation method, preparing tungsten, molybdenum and aluminum precipitates by a parallel flow precipitation method, mixing the nickel and aluminum precipitates with the tungsten, molybdenum and aluminum precipitates, performing ageing, adding urea while performing hydrothermal treatment, then performing shaping and the like so as to prepare the catalyst. The catalyst prepared by the method is high in content of surface phase active metal, and high in active site density, the active metal is uniformly dispersed, the active metal is well coordinated and matched, the utilization rate of the active metal is high, and the pore structure of the catalyst is reasonable. The catalyst is high in mechanical strength, has higher hydrodesulfurization and hydrodenitrogenation reaction properties, and is particularly suitable for being used in ultra-deep hydrodesulfurization and denitrification reactions of diesel fractions.