The present invention discloses a method for preparing glucosyl steviol glycosides through enzymatic catalysis under programming temperatures in high throughput, belonging to the technical field of biosynthesis of sweeteners. By using cyclodextrin glucosyltransferase from Geobacillus sp. as a catalyst, steviol glycosides as the glycosyl receptor and dextrin or oligosaccharide as the glycosyl donor, taking a calcium/barium ion salt bridge as the main stabilizer and combining with glycerol to adjust the conformation and binding domain openness of the enzyme, and utilizing transglucosylation and hydrolytic activities of amylase at variable temperatures in different stages, thereby preparing the glucosyl steviol glycosides through enzymatic catalysis under programming temperatures in high throughput. The technology of the present invention can improve the utilization rate of the enzyme, and obtain glucosyl steviol glycosides with good sweetness and good taste.