The invention discloses a preparation method of a small-crystal-particle NaY molecular sieve. Hexamethylenetetramine is used as an additive, and the small-crystal-particle NaY molecular sieve is prepared in a segmental crystallization method. The method comprises the following steps: mixing a silicon source and an aluminum source, standing and aging for 2 to 72 hours at 5 to 60 DEG C to obtain a guide agent; then mixing the silicon source, the guide agent, the aluminum source and the hexamethylenetetramine to form cement, wherein in the reaction mixture gel, the molar ratio of Na2O, Al2O3, SiO2, H2O and C6H12N4 is (0.5-1):1:(5-40):(80-800):(0.5-10); static crystallizing in two segments under different temperatures, wherein the first-segment crystallization temperature is 60 to 85 DEG C, crystallizing for 12 to 48 hours, the second-segment crystallization temperature is 90 to 120 DEG C, and crystallizing for 12 to 72 hours; and finally filtering, washing and drying to obtain the small crystal-particle NaY molecular sieve. The relative crystallinity of the prepared composite molecular sieve is greater than 85 percent, and the size of a crystal size is 400nm to 600nm. The preparation method is easy for obtaining raw materials, low in preparation cost and good in industrial application prospect.