Amorphous carbon-based sulfonated catalysts were generated from four kinds of biomass (lignin, cellulose, wood meal and D-xylose) by hydrothermal carbonization at various temperatures (225, 245 and 265 °C) followed by sulfonation, with a yield of 36–56%. All of these catalysts showed aromatic structure, hydroxyl and carboxyl groups, with a density of SO3H groups between 0.56 and 0.87 mmol g−1. 5-Hydroxymethylfurfural (HMF) was produced from inulin in ionic liquids (ILs) in one step with the addition of carbon-based sulfonated catalysts, with a factual yield of 47–65% at 100 °C, 60 min. Moderate extension of reaction time (from 30 to 90 min) and increase of temperature (from 80 to 120 °C) promoted HMF production. Ethyl acetate was used as extractant, and about 39–55% of HMF can be recovered from ILs. One problem with these carbon-based sulfonated catalysts was that they would be partly deactivated in ILs for separate reuse, however, they can be easily regenerated by dilute sulfuric acid treatment. The carbon-based sulfonated catalysts exhibited good catalytic activity compared with traditional solid acid catalysts, and the carbon-based sulfonated catalyst/ILs reaction system showed high reusability. In consideration of the renewable as well as the high catalytic activity abilities, these biomass derived carbon-based sulfonated catalysts would be promising for industrial application.