The invention relates to a method for preparing high-purity fruit fructose. The method comprises the following steps: (1) testing the quality of fruit; (2) washing the fruit; (3) crushing; (4) performing enzymolysis; (5) performing membrane concentration; (6) decoloring; (7) desalting; (8) performing isomerization purification; (9) performing aftertreatment; (10) performing finished product filling. The content of fructose of a product prepared by using the method is higher than 90%, and the product is high in color value stability, low in production cost and small in waste liquid discharge amount.