Display omitted •Cotton gin trash catalyst is effective in the dehydration of fructose to HMF.•Cotton gin trash catalyst consists of 3 aromatic layers, –COOH and –SO3H groups.•The reusability of cotton gin trash derived catalyst is >5 times.•Fructose was transformed via a carbaldehyde intermediate prior to dehydration.•Adsorption mechanism of catalyst goes by liquid film and intra-particle diffusions. Biomass-derived carbon catalysts have been extensively studied for the dehydration of sugars to platform chemical 5-hydroxymethyl furfural (HMF), which can be used to produce valuable chemicals and fuels. However, only limited studies have been conducted to determine their carbon molecular structures and how these influence the conversion process. Here, we prepare a chlorosulfonated carbon catalyst derived from cotton gin trash (CGT) at 400 °C for the dehydration of fructose to produce 5-hydroxymethyl furfural (HMF) in the ionic liquid, 1-butyl-3-methyl-imidazolium chloride (BMIMCl). The highly efficient chlorosulfonated carbon catalyst consisting of 3 aromatic layers of furanic, phenolic rings and aliphatic–aromatic carbon structures with –COOH, phenolic OH, -SO3-, and -SO3H functional groups were found to have a similar performance as the commercial catalyst, Amberlyst-15. The carbon material was reused 5 times without loss of catalytic activity. The formation of the sugar intermediate, 3,4-dihydroxy-5-hydroxymethyl-tetrahydrofuran-2-carbaldehyde may be related to –COOH and phenolic OH groups forming hydrogen bonds with fructose, and the adsorption of fructose onto the graphitized sp2 internal carbon regions where interactions with the defects in the carbon material occur.