Ionic liquids (ILs) as additives were used in the selective conversion of bio-based carbohydrates to 5-hydroxymethylfurfural (HMF) in this work. The effect of adding various imidazole-based ionic liquids with different anion structures on the production of HMF from fructose was firstly investigated in aqueous media. The presence of 15 wt% 1-butyl-3-methylimidazole chloride ([Bmim]Cl) ionic liquids in water with Fe-2(SO4)(3) as the homogeneous catalyst provided a more effective HMF synthesis compared to that without [Bmim]Cl addition. The enhanced HMF yield was mainly attributed to the fact that [Bmim]Cl might play a vital role in stabilizing the HMF molecule, which could thereby suppress side reactions involving HMF (e.g., its rehydration to levulinic acid or/and polymerization to humins). NMR and FTIR analyses suggested that such a stabilization effect stemmed from the interaction of [Bmim]Cl with the hydroxyl and aldehyde groups of HMF through hydrogen bonding. By performing the operation in a biphasic system (i.e., with the biomass-derived THF solvent as the organic phase and the addition of NaCl salt into water for improving HMF partition), the HMF yield over the Fe-2(SO4)(3) catalyst in the presence of the [Bmim]Cl additive could be further improved. The catalyst and ionic liquids were quite stable, and could be reused for more than five cycles with a consistent activity. A similar enhancement effect of [Bmim]Cl was also demonstrated in HMF synthesis with better yields from other biomass feedstocks or derivatives (including glucose, sucrose, cellobiose, inulin and starch) in aqueous media.