Sucrose-6-acetate, a short-chain monoester, is an important intermediate for the preparation of sucralose. Regioselective transformations of mono- and oligosaccharides by enzymes have been performed in organic solvents. The present study was carried out with Candida rugosa lipase to synthesize sucrose-6-acetate by transesterification of sucrose and vinyl acetate in a two-phase system consisting of a buffer solution and an organic solvent. The screening results revealed that 2-butanol/Tris-HCl was the optimal two-phase system for biocatalysis, and other factors influencing the synthesis of sucrose-6-acetate were also studied. Three major factors (temperature, initial buffer pH, and molar ratio of substrates) were identified through Plackett-Burman design, and the response surface methodology was employed to optimize the reaction process. Under optimal conditions, the yield of sucrose-6-acetate reached up to 57.42%. The aqueous two-phase system was successfully applied to the synthesis of sucrose-6-acetate with high yield, low toxicity, good resolution, low cost, and simple scale-up.