A combined experimental and computational study on the imidazolium ionic liquid-promoted conversion of d-Glucosamine (GlcNH2) to deoxyfructosazine (DOF) and fructosazine (FZ) was performed. The pathways for the formation of DOF and FZ via self-condensation of GlcNH2 were investigated by in situ13C NMR using site-selectively 13C-labeled GlcNH2. The structural characterization of the reactive species by ESI–MS spectrometry combined with NMR analysis of [13C-1]GlcNH2 indicates that the first carbon (C-1) of GlcNH2 maps onto the corresponding ring carbons of the intermediate, called dihydrofructosazine [2,5-bis(d-arabino-tetrahydroxybutyl)dihydropyrazine], which subsequently is converted to the corresponding pyrazine ring carbons of DOF and FZ respectively. The isotopic-labelling experiments disclose that there are two parallel reaction pathways open to the intermediate dihydrofructosazine, when the reaction takes place in DMSO with [C2C1Im][OAc] as catalyst. The theoretical results from DFT calculation indicate that the role of the imidazolium based ILs [C2C1Im][OAc] can be envisaged as an acid-base dual activation in catalyzing DOF and FZ formation. It turns out that the acidic cation center exerted significant influences on the energy barriers associated with dehydration reaction. In addition, a critical role of counteranion AcO− is to facilitate dehydrogenation process, leading to the formation of hydrogen. A comparison between the two reaction channels, after the formation of intermediate dihydrofructosazine, indicates that both pathways are plausible and that the pathway to DOF is thermodynamically more favorable than that to FZ. The theoretical results are consistent with the experimental observations, and therefore, a detailed and reasonable reaction mechanism was proposed