A series of organic sulfonate inner salts, viz., aprotic imidazolium-and pyridinium-based zwitterions bearing sulfonate groups (−SO 3 − ), were synthesized for the catalytic conversion of fructose-based carbohydrates into 5-hydroxymethylfurfural (HMF). The dramatic cooperation of both the cation and anion of inner salts played a crucial role in the HMF formation. The inner salts have excellent solvent compatibility, and 4-(pyridinium)butane sulfonate (PyBS) affords the highest catalytic activity with 88.2 and 95.1% HMF yields at almost full conversion of fructose in low-boiling-point protic solvent isopropanol (i-PrOH) and aprotic solvent dimethyl sulfoxide (DMSO), respectively. The substrate tolerance of aprotic inner salt was also studied through changing the substrate type, demonstrating its excellent specificity for catalytic valorization of fructose-moiety-containing C6 sugars, such as sucrose and inulin. Meanwhile, the neutral inner salt is structurally stable and reusable; after being recycled four times, the catalyst showed no appreciable loss of its catalytic activity. The plausible mechanism has been elucidated based on the dramatic cooperative effect of both the cation and sulfonate anion of inner salts. The noncorrosive, nonvolatile, and generally nonhazardous aprotic inner salt used in this study will benefit many biochemical-related applications.