Polydatin, a 3-O-glucoside of resveratrol, shows an enhanced aqueous solubility and bioactivity. The UDP-glucose-dependent glycosyltransferase UGTBL1, derived from Bacillus licheniformis ZSP01, glycosylates resveratrol but exhibits promiscuous regioselectivity. To regulate the region-specific glycosylation of resveratrol, this study employed a strategy involving deletion modification. Specifically, the amino acids 62I and 63D, located on the loop, were deleted to create the mutant Δ(62-63), resulting in an increase in polydatin's regioselectivity from 12.2% in the wild type to around 90.0%. Molecular docking and dynamics simulations were conducted to analyze the local flexibility of this region. This flexibility brings the protein skeleton closer to the active center, facilitating interactions between the 3-OH group of resveratrol and the amino acid residues surrounding the active center, ultimately promoting the formation of polydatin.