Ionic liquids are extensively used in many separation processes due to excellent dissolving ability for organic compounds and polymer materials, such as cellulose dissolution, Keratin dissolution. However, during the dissolution process, a small amount of degraded organic saccharides was produced, which could affect the strength of the regenerated fibers. Thus, it is required to find a suitable method for the removal of these saccharide molecules during the process of IL recovery. In this study, electrodialysis (ED) was used for the separation of these saccharide molecules from IL aqueous solution. In order to evaluate the separation performance of ED process, the influences of applied voltage, initial concentrations of IL and saccharide, and the initial volume ratio of the dilute solution to the concentrated solution on the current efficiency (eta), recovery ratio (R-IL), removal ratio (R-S) and energy consumption (E) were systematically investigated. Experimental results showed that ED played a dual role in removing saccharides from the IL aqueous solution and concentrating IL. Under the optimized conditions, the removal efficiency of saccharides was 98.11% and IL concentration ratio is 2.63. Especially, the characterization results identified that the structure of the recovered IL was in well agreement with that of the fresh IL. All of these proved that ED might be an effective and green method to realize the separation of saccharides from the IL aqueous solution.