Considering the contemporary interests of water-free reverse micelles (RMs) in the field of organic reaction medium and potential drug delivery carrier, we synthesized two different classes of ionic liquids (ILs), protic N-methyl-2-pyrrolidonium hexanoate, [NMP][Hex], and aprotic choline hexanoate, [Chl][Hex], and subsequently incorporated them in a mixture of polyoxyethylene (20) sorbitan monooleate (Tween-80) and cyclohexane. In order to understand the differential nature of interinterionic interaction of two ILs, we performed DFT calculations on pure ILs to correlate with experimental results. The formation of IL-in-oil RMs was confirmed from phase behavior and DLS studies. Interestingly, [NMP][Hex]-based systems showed a larger monophasic region and droplet size along with higher shear viscosity compared to [Chl][Hex]-based systems. Stronger interaction between [NMP]+ and Tween-80 due to their protic nature might be the driving force for such observations which supported the resonance stabilization energy [E(2)] and charge population analysis by NBO calculation. Smaller E(2) values along with lesser NBO charges on atoms involved in H-bonding in pure [NMP][Hex] than [Chl][Hex] corroborated with the experimental observations. This primary hypothesis was further confirmed from FTIR and time-resolved fluorescence studies. These systems showed efficient thermal stability. Taking all of the results together, we anticipate that these RMs could be used as efficient delivery systems and for nanomaterial synthesis.