The study was carried out to evaluate the extraction efficiency of ferulic acid (FA) and vanilla acid (VA) from aqueous phase into IL phase. To achieve the highest extraction efficiency, the influence of varying key parameters was evaluated and optimized by response surface methodology based on Box-Behnken design, including phase volume ratio, extraction temperature and extraction time. FA (or VA) extraction under the optimal conditions were: phase volume ratio of 1.38 (1.28), extraction temperature of 66.34 °C (49.28 °C) and extraction time of 33.83 min (36.64 min) under optimum conditions an average extraction efficiency of 97.11 ± 1.05% for FA was achieved, while VA was 85.43 ± 1.62%. This was very close to the predicted value from the model, 98.05% (86.16%). Additionally, recycling and utilization of ILs were performed well with the recovery ratio for 81.0%. Based on thermodynamic analysis, FTIR and 1H NMR analysis, the combination of hydrophobic interaction and hydrogen-bond interaction resulted in the real extraction result above. It is desirable to provide a useful reference for the separation and purification of FA, VA, and extend the potential application of ionic liquid in the separation of natural active compounds with great prospects.