A survey on the effect of ionic liquids (ILs) over the thermal stability of a heavy Mexican oil was performed. ILs used were based on [Cnim]+ and [Cnpyr]+ organic cations with FeCl4− metal anion. Mixtures of heavy crude oil (HCO) with ILs show three oxidation zones: low temperature oxidation (LTO), full deposition (FD) and high temperature oxidation (HTO). Thermal stability and mass loss decrease in the LTO zone but increase in the FD and HTO zones for every ILs used. The activation energy of the oxidation is influenced by the ILs in the HTO zone. It decreases when increasing the size of the organic radical substitute in the cation of the ILs while it increases with the presence of hydroxyl groups. The influence of electronic structure and reactivity indexes are rationalized to understand the variations of activation energy obtained of the reaction systems. Among all cations used, cation-3 (IL-3) shows the greater value of HOMO-LUMO gap as well as the lower activation energy.