The invention relates to a preparation method of crystalline fructose, which sequentially comprises the following steps: carrying out chromatography separation on fructose-glucose syrup, carrying oution exchange and nanofiltration operation on the obtained fructose liquid, then respectively carrying out concentration through a double-effect plate type evaporator and a scraper evaporator, mixing the concentrated fructose liquid with ethanol and finally carrying out crystallization, centrifugal separation and drying, thereby obtaining the crystalline fructose. The prepration method of the crystalline fructose adopts the nanofiltration separation technology, removes impurities which affect the crystallization and the quality of a finished product before the crystallization, improves the product quality and the crystallization yield, combines the high-efficient plate type evaporator with the scraper evaporator, reduces the evaporation temperature of the fructose and the residence time inthe evaporators and effectively prevents the thermal decomposition and the complex reaction of the fructose. Compared with the prior art, the crystalline fructose produced by the method has the advantages of high purity of the fructose, uniform crystalline particles, good color and luster, high crystallization rate and low unit cost.