The invention discloses a method for synthesis of a high silica-alumina ratio ultrafine NaY molecular sieve. The method comprises the following steps of collecting a crystallization mother liquor of a high silica-alumina ratio ultrafine NaY molecular sieve, adding inorganic acid and soluble aluminum salt solution into the crystallization mother liquor so that pH is adjusted and silica-alumina gel precipitates are formed, filtering the precipitates to obtain silica-alumina gel filter cake with a SiO2/Al2O3 ratio of 17-85, preparing a guiding agent from a part of or all the filter cake, adding reaction gel with a silicon source, an aluminum source and water into the guiding agent, and carrying out at least three programming calefactive control crystallization processes under full dynamic conditions. The NaY molecular sieve has average crystal grain sizes of 100-500nm and a skeleton silica-alumina ratio (SiO2/Al2O3) higher than 6.7. The method realizes silicon source complete cycle utilization.