The invention relates to a method for synthesizing a kaolin microsphere in-situ crystallized product containing small crystal grain NaY molecular sieves. Kaolin is used as a raw material. The method comprises the following steps of: adding deionized water and sodium silicate or sodium pyrophosphate into the kaolin, mixing and slurrying, performing spray drying on the mixed slurry to prepare kaolin spray microspheres with particle diameters of 20 to 110 microns, roasting a part of the kaolin spray microspheres for 1 to 3 hours at the temperature of between 920 and 1,000 DEG C to obtain high-temperature roasted microspheres, and roasting the other part of the kaolin spray microspheres for 1 to 3 hours at the temperature of between 700 and 900 DEG C to obtain metakaolin microspheres; mixing the high-temperature roasted microspheres and the metakaolin microspheres in a mass ratio of 9:1-1:9, adding sodium silicate, directing agent, sodium hydroxide solution, deionized water and organic additive into the mixture, and crystallizing for 16 to 36 hours at the temperature of between 90 and 95 DEG C; and filtering, removing mother solution, and drying the filtrate to obtain the kaolin microsphere in-situ crystallized product containing NaY molecular sieve crystal grains of 200 to 400 nanometers.