The invention discloses a hydrocracking catalyst and a preparation method thereof. The hydrocracking catalyst comprises: a carrier composed of a modified beta molecular sieve, a modified Y type molecular sieve and alumina, and hydrogenation active metal components. Specifically, the modified beta molecular sieve is prepared by: subjecting a crystallized beta molecular sieve slurry directly to ammonium exchange and a template agent removal treatment, then first conducting a hydrothermal treatment, and performing an aluminum salt solution treatment, under the condition of maintaining a high beta molecular sieve crystallinity, removing part of non-framework aluminum uniformly, thus obtaining the beta molecular sieve with the characteristics of high Si / Al ratio, large specific surface area, appropriate acidity and acid distribution, and reasonable structure, etc. The modified beta molecular sieve especially has a suitable cracking effect and a very good isomerization effect on long-chain alkane and the long side chain alkyl of aromatic hydrocarbon and cyclane, and has a synergistic effect with the Y type molecular sieve, so that the hydrocracking catalyst can have very high catalytic activity and middle distillate selectivity. And the condensation point of diesel fraction is substantially reduced, and the product properties of middle distillate are improved.