In order to overcome the elementary heterogeneous nucleation while octahydro trisodium salt of fructose-1,6-diphosphate(FDPNa3.8 H2O) is crystallized with ethanol precipitation at low temperature, a new crystallization method with alcohol precipitation combined with salt precipitation has been presented. The ethanol-sodium acetate system for crystallization of salt of fructose-1,6-diphosphate is based on the mechanism of crystallization of FDPNa3.8 H2O in the ethanol-low temperature system. It is found that crystal size may be controlled by regulating temperature or pH value of solution in the crystallization process, and the crystal yield increases to 95% from 78% which obtained in the ethanol-low temperature system.