Accurate prediction of physicochemical properties of ionic liquids (ILs) is of great significance to understand and design novel ILs with unique properties. This study employed the electrostatically embedded generalized molecular fractionation (EE-GMF) method for accurate energy calculation of IL clusters. The accuracy and efficiency of the EE-GMF method are systematically assessed at different ab initio levels (including HF, DFT and MP2) with diverse basis sets. With the fixed charge model for the embedding field, the deviations of the EE-GMF approach from conventional full system calculations are within 2.58 kcal mol-1 for all IL clusters with up to 30 ion pairs (720 atoms), tested in this study. Moreover, this linear-scaling fragment quantum mechanical (QM) method can significantly reduce the total computational cost for post-HF methods. The EE-GMF approach is well-suited for studying the energetic, structural and dynamical properties of ILs using high-level ab initio theories.