Background Ionic liquids (ILs) have advantages in terms of flexible structure and composition for the whole cell mediated biocatalytic reaction. However, the lack of design strategy for ILs has hampered the development of biocatalysis in non‐aqueous medium. In the present study, to establish an efficient reaction system to obtain vital chiral compounds, a novel IL was designed by combining the superior characteristics of quaternary ammonium‐ and dialkyl‐based cationic surfactant IL to enhance the recombinant Escherichia coli cells‐catalyzed bioreduction efficiency. Results [HOEtN1,1,1][BF4] was synthesized and showed excellent characteristics of low toxicity to the biocatalyst, reduced toxicity of substrate to the microbial cells and moderate increase of cell membrane permeability. In the [HOEtN1,1,1][BF4]‐ containing reaction system, some valuable factors involved in the biocatalytic reduction of ethyl 4‐chloro‐3‐oxobutanoate to ethyl (S)‐4‐chloro‐3‐hydroxybutanoate were found to be: 2.5% (w/v) [HOEtN1,1,1][BF4], 20% (v/v) isopropanol, 3 M COBE, pH 7.0, 30 °C, reacted for 16 h. A yield of 96.7% was obtained under the optimum conditions with above 99% enantiomeric excess value, and the proposed bioprocess was also successfully scaled up to a 5 L fermentor with a yield of 90.7%. Conclusion The developed IL [HOEtN1,1,1][BF4] is a promising solvent for enhancing the efficiency of model bioreduction. It was also evaluated for broadening its application to the biosynthesis of (R)‐[3,5‐bis(trifluoromethyl)phenyl] ethanol catalyzed by recombinant Escherichia coli, with remarkable success. © 2018 Society of Chemical Industry