An effective approach was developed to biotransform luteolin glycosides in hydrophilic organic solvents. Bacillus cereus A46 cells showed high activity and stability in 5–20% (v/v) DMSO with 90–98% conversion rates of luteolin glycosides. Five glycosides of luteolin 7-O-β-glucoside, luteolin 4′-O-β-glucoside, luteolin 3′-O-β-glucoside, luteolin 7,3′-di-O-β-glucoside and luteolin 7,4′-di-O-β-glucoside were obtained. The addition of DMSO greatly promoted the solubility of luteolin and further regulated the formation of the main products from five luteolin glycosides to luteolin 7-O-β-glucoside (931.2 μM). Fourteen flavonoids and anthraquinones were used as tentative substrates. Glycosylation positions were located at the C-7, C-3′ or C4′ hydroxyl groups of flavonoids and C-5 hydroxyl group of anthraquinones. The 3′,4′-dihydroxy arrangement played the key role for the antioxidant activity of luteolin.