The invention relates to a hydrogenation catalyst and a preparation method thereof. The active metals are the VIB group metal and VIII group metal, the carrier is composed of a composite molecular sieve, alumina, silicon dioxide and a binder, and the composite molecular sieve is an hierarchical porous composite molecular sieve formed by cladding a microporous Beta molecular sieve with mesoporous amorphous silicon-aluminum. The preparation method of the hydrogenation catalyst includes: (1) mixing the composite molecular sieve, alumina, silicon dioxide and the binder evenly to conduct molding; performing drying in an atmosphere of 80-130DEG C, and conducting roasting at 400-600DEG C; and (2) preparing an impregnation solution from a compound containing active metal component elements, dipping the carrier, then drying the carrier at 80-130DEG C, and conducting calcination at 400-600DEG C. The catalyst is used for hydrocracking reaction of vacuum distillate oil, improves the reaction catalytic activity, promotes selective generation of middle distillate oil, effectively inhibits secondary cracking side reaction, and reduces the yield of low-boiling-point distillates.