The invention discloses a preparation method of a nitrogen-resisting hydrocracking catalyst. The preparation method comprises the following steps: 1, uniformly mixing a modified Y type molecular sieve, amorphous silicon-aluminum and/or aluminum oxide, adding dilute nitric acid, carrying out slurrying, then performing extrusion molding, and performing drying and calcination to obtain a silicon-aluminum carrier containing the modified Y type molecular sieve; and 2, performing impregnation on the carrier of the step 1 by adopting impregnation liquid containing an active metal, drying the impregnated carrier and calcining the dried carrier to obtain the hydrocracking catalyst, wherein the modified Y type molecular sieve has the following characteristics: the crystal cell constant of the modified Y type molecular sieve is 2.425-2.455nm; the bulk phase silicon-aluminum ratio is 8-30, wherein the surface layer silicon-aluminum ratio is 20-80, and the surface layer silicon-aluminum ratio is higher than the bulk phase silicon-aluminum ratio; and the specific surface area of the modified Y type molecular sieve is 600-800m<2>/g, and the pore volume is 0.40-0.70ml/g. The hydrocracking catalyst prepared by the preparation method disclosed by the invention has good reactivity and nitrogen resistance, and can be applied to different hydrocracking reaction processes such as a process for increasing the production of diesel oil, a process for increasing the production of chemical raw materials, and a process for catalyzing diesel oil hydro-conversion and the like.