Whole-cell based biocatalysis in ionic liquids (ILs)-containing systems has attracted increasing interests in recent years. Compared to bioreactions catalyzed by isolated enzymes, the major advantages of using whole cell in biocatalytic processes are that cells provide a natural intracellular environment for the enzymes to function with cofactors regeneration in situ. An increasing number of renewable ILs are now accessible as a result of the ongoing progress in designing strategy of ILs and the sustainable environment requirement. The toxicity of ILs to microbial cells and the biodegradability are two of the crucial factors which allow the biocatalysis in ILs being applied in practice rather than in bench-scale. Applications of whole-cell biocatalysis in IL-containing system have, to date, been focused on the production of valuable compounds, mainly through reduction, oxidation and hydrolytic reactions. The mechanism research of ILs affecting the whole-cell biocatalysis offer the possibility to effectively integrate ILs with biotransformation. Thus, a comprehensive understanding of the whole cell-based biocatalytic process with ILs will contribute to the discovery of novel solvent for enzymatic reaction and the synthesis of more valuable compounds.