The invention discloses a small crystal particle Y-shaped molecular sieve and a preparation method thereof. The property of the small crystal particle Y-shaped molecular sieve is as follows: the molar ratio of Si, O2 / Al2O3 is 10.0-120.0, the cell parameters are 2.420-2.445 nm, the crystallization retention is larger than 95 percent, and B acid / L acid is above 7.0. Due to higher raw material thermal and hydrothermal stability, higher silicon-aluminum ratio, good stability and uniform framework silicon-aluminum structure, the small crystal particle NaY molecular sieve can ensure the framework continuity of the molecular sieve, reduce the collapse possibility of the framework structure and maximally keep the integrity of a silicon-aluminum-oxygen structure in the modification, namely in the ammonia exchange, ammonium fluorosilicate dealumination and silicon reinsertion, hydro-thermal treatment, aluminum salt and acid mixed water solution treatment process, thereby having high crystallization retention. The Y-shaped molecular sieve can be taken as an active component of a hydrocracking catalyst, thereby improving the activity of the catalyst, the selectivity of the molecular sieve and the product quality.