Starch， as one of the important staple foods for our population， provides the main source of energy for the organism. Glycogen branching enzyme (GBE， EC 2.4.1.18) is an important glycosyltransferase for enzyme-modified preparation of branched starch， which connects starch short-chain fragments with α-1，6 glycosidic bonds to the main chain connected with α-1，4 glycosidic bonds through transglycosylation. Most of the existing methods of enzymatic starch modification are based on the pasting systems， but high temperature pasting destroys the crystalline structure of starch. The crystalline structure of starch has an important influence on the characteristics of food processing applications. In this paper， glycogen branching enzyme derived from Pyrococcus horikoshii OT3(Ph) was used to modify three different crystalline starches， corn starch (CS)， potato starch (PS)， and pea starch (PBS)， based on a non-pasteurized system， and the structure and digestive properties of the products were analyzed. The results showed that the modification effect of Ph GBE on the three starches was CS＞PBS＞PS. GBE modification decreased the relative crystallinity and the content of straight-chain starch of the products， and increased the proportion of α-1，6 glycosidic bonding and the length of branched chain (DP＜13)， which resulted in the improvement of starch digestive characteristics and the increase of pasting temperature. Therefore， GBE has good application prospects in the modified starch industry.