Ionic liquids (ILs)-assisted microbes and enzymes represent an effective approach for the conversion of lignocellulosic biomass into fermentable sugars in a biorefinery. Comparative transcriptome analysis revealed that A. terreus NEAU-7 could reduce the adverse effects of intracellular ILs through promoting ion transport and increasing compatible solutes. The strain could prevent extracellular ILs through obtaining more metabolic energy and reducing the permeability of cell membrane This work is critical for the exploration of ILs-resistance mechanism for lignocellulolytic fungi, which contributes to the successful employments of ILs-assisted fungi in the degradation of lignocellulosic biomass into valuable products.