The main objective of this study is to provide an in-depth analysis that reveals the impact of thermal treatment on the different functional groups that exist in asphaltene molecules. This contribution is important to further understand the nature of changes that take place in asphaltenes during distillation and thermal cracking processes. A slight increase was observed in the aromatic -CH groups, compared to aliphatic -CH groups, as crude oil is processed to atmospheric and vacuum residues. A slight decrease was also observed in the intensity ratio between methylene and methyl groups (CH2/CH3) with distillation, which suggests a decrease in the average length of alkyl side chains for asphaltene molecules. The Fourier transform infrared (FTIR) results also suggest the possibility of thiophenic compounds oxidation during the atmospheric and vacuum distillations. More obvious differences were noted between asphaltenes exposed to thermal cracking, separated from the pitch samples, and their parent asphaltenes from the vacuum residues. Although the spectra of thermally treated asphaltenes have most of the features that belong to their parent asphaltenes, the results illustrate more aromatic structures as the reaction severity increases. In addition, the ratio of CH3 to CH2 groups shifted toward CH3 with increasing reaction time and/or temperature due to the shortening of alkyl side chains. FTIR results have been further supported by H-1 and C-13 nuclear magnetic resonance (NMR) analysis, which confirmed the conclusion that thermal cracking of residual oils mainly affected the paraffinic side chains while the observed changes in the aromatic core appear to be relatively limited.