As a nutritious fruit, mulberry is an ideal source of high-quality cyanidin-3-O-glucoside (C3G) with various biological activities. However, the difficult separation process of high-purity C3G leads to its high price. To rapidly prepare high-purity C3G, cyanidin-3-O-rutinoside is converted to C3G by direct hydrolysis of rhamnose bond using a whole-cell catalyst containing α-rhamnosidase. Combined with an aqueous two-phase system, a coupling reaction separation system was established. Two monomers were successfully separated by semi-preparative high performance liquid chromatography (semi-preparative HPLC). The conversion of C3G catalyzed by whole-cells in the PEG/Na2SO4 system increased from 47.11 % to 66.56 %, compared with the EtOH/(NH4)2SO4 system, and the whole-cell activity remained above 50 % after five rounds of reuse. Meanwhile, the purity of C3G was increased to 99 % via the semi-preparative HPLC purification and identified by MS. Thus, an integrated process of whole-cell-catalyzed conversion and product peak cutting partition collection provides a novel strategy for efficient biomanufacturing of high-purity C3G.