The invention relates to a method for preparing trehalose crystals. A trehalose aqueous solution is subjected to vacuum evaporation and concentration, trehalose seed crystals are added, the temperature is controlled, simultaneously an elution agent is added in a flowing mode to enable the supersaturation degree of the solution to be maintained in a low level, and the temperature is reduced gradually to achieve crystallization. The trehalose crystals are produced by means of an elution-cooling coupling crystallization method, and the crystallization yield of trehalose is improved. Fine crystals are prevented from being produced in the crystallization process, and obtained products are even in fineness distribution and high in purity. Compared with traditional coupling crystallization, a crystallization period is shortened, the crystallization yield is improved, and convenience is further provided for follow-up centrifugal separation. The novel method for preparing the trehalose crystals has large application potential in the field of functional sugar crystallization production.