Previous phytochemical studies showed that the major flavonoids in Scutellaria baicalensis are baicalin, baicalein, wogonoside and wogonin. The two glycosides (baicalin and wogonoside) can be transformed into their aglycons (baicalein and wogonin), which possess positive anticancer potential. In this study, we used glycosidase to catalyze flavonoids in S. baicalensis to enhance the herb's anticancer activities. Our HPLC data showed that, using the optimized conditions obtained in our experiments (20 U/g of cellulase, 50˚C, pH 4.8 and treatment for 8 h), there was a marked transformation from the two glycosides to their aglycons. The anticancer activity was subsequently evaluated using a series of S. baicalensis extracts in which variable lengths of glycosidase treatment time were used. Combining analytical and bioassay results, we observed that the higher the aglycon content, the stronger the antiproliferation effects. Compared to the untransformed control, 8 h of glycosidase catalyzing significantly increased antiproliferative activity on human colorectal and breast cancer cells, and its cancer cell growth inhibition is, in part, mediated by cell cycle arrest at the S-phase and induction of apoptosis. Data from this study suggest that using glycosidase to catalyze S. baicalensis offers a promising approach to increase its anticancer activity.