The invention provides a hydrocracking catalyst containing a Y molecular sieve and a preparation method thereof. A catalyst carrier contains a high dispersed Y molecular sieve, and active components of the catalyst comprise one or more of W and Mo and one or more of Ni and Co. In preparation of the high dispersed Y molecular sieve, a certain amount of a surfactant is added into a final synthetic mixture. The preparation method can efficiently and conveniently produce the high dispersed Y molecular sieve and the hydrocracking catalyst. Compared with the prior art, the preparation method is simplified, improves selectivity of the hydrocracking catalyst on the basis of sufficient activity and improves a desired product yield.