The present invention relates to a composition for epimerization of a hexose biphosphate, comprising a thermophile-derived sugar epimerase, and a method for preparing a hexose biphosphate epimer using the composition. The thermophile-derived sugar epimerase according to the present invention can effectively derive an epimerization reaction of a hexose biphosphate and can easily produce an epimer form of the hexose biphosphate, in particular a rare sugar hexose, and thus can be usefully utilized in the pharmaceutical and food industry.