The invention discloses a hydrocracking catalyst and a preparation method thereof. The catalyst comprises hydrogenation active metals and a carrier containing modified Y molecular sieve, alumina and amorphous aluminium silicon, wherein, the Y molecular sieve is prepared by the following method: the Y molecular sieve undergone hydro-thermal treatment by mixed water solution of aluminium salt and acid is adopted; the performance of the Y molecular sieve is as follows: specific surface is 800m<2>/g-900m<2>/g, total aperture volume is 0.40ml/g-0.50ml/g, relative crystallinity is 90%-130%, cell parameter is 2.434-2.440nm, aluminium silicon mol ratio is 20-100, infrared acid volume is 0.3-0.8mmol/g, the mol ratio of acid B and acid L is above 7.0, sodium oxide content is less than or equal to 0.05wt%. The catalyst prepared by the invention has the advantages of high catalytic activity, good target product selectivity and can produce heavy naphtha, aviation fuel and diesel fuel, and the like, with high yield and good quality.