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(<i>S</i>)-3,5-Bistrifluoromethylphenyl ethanol((<i>S</i>)-BTPE) is a key pharmaceutical intermediate of the NK-1 receptor antagonist. The asymmetric bioreduction of 3,5-bis(trifluoromethyl) acetophenone (BTAP) to (<i>S</i>)-BTPE using <i>Rhodococcus erythropolis</i> XS1012 has been established in a phosphate buffer system. To overcome the problem of unsatisfactory yields at high substrate concentration, deep eutectic solvents (DESs) have been introduced to the buffer system. After screening 13 kinds of choline chloride-based DESs, [choline chloride][urea] ([ChCl][U]) showed great influence on the cell activity and significantly increased the cell membrane permeability. Subsequently, some major parameters for this reaction were determined. A remarkable (<i>S</i>)-BTPE yield of 91.9% was gained at 150 mM substrate concentration under optimized reaction conditions with &gt;99.9% product enantioselectivity. Compared to reduction in a buffer system, the developed [ChCl][U]-containing system increased the yield from 82.6% to 91.9%. It maintains a yield of 80.7% with the substrate concentration up to 300 mM, compared to only 63.0% in buffer system. This study demonstrated that [ChCl][U] is a feasible co-solvent to improve the bioreduction process.