The understanding of intermolecular interactions on asphaltene nanoaggregates has important implications over the petroleum industry. Here, we investigated the aggregation of asphaltene and resin using a hierarchical approach that combines Density Functional Theory (DFT) with dispersion corrections and molecular mechanics (MM) calculations. From molecular models already established in the literature for specific types of asphaltene (A) and resin (R) molecules, we employed MM simulations to calculate the potential energy surface to obtain the best conformations for the possible dimers A-A, A-R, and R-R, as well as the relevant combinations of trimers A-R-A, A-A-R, and A-A-A, which have been further relaxed by the DFT calculations. Indeed, the formation of the dimer A-A is energetically more favored with respect to A-R and R-R mainly due to the enhanced effect on the intermolecular interaction of the aromatic region of A. In this context, the trimers have shown to be almost 3 times more stable than the dimers. Our result suggests that the nanoaggregates have a charge density well distributed but centralized between the aromatic ring 7r-orbitals, whereas A molecules are added, creating a tightly packed structure. In this case, the contribution from the aliphatic chains is just steric to stabilize the aggregate and shield the aromatic center for new interactions. Although the,pi-pi stacking can guide the nanoaggregate formation, the presence of the R molecule leads to a possible disaggregation. When R molecules are inserted, the growth of the nanoaggregate seems to be yet continued due to a dipole moment and radius of gyration increasing. However, we observed charge rearrangement from the aromatic center of pi-pi interaction; to aliphatic chains with heteroatoms that displaces into the structure. The HOMO-1 and HOMO degeneracy is broken in this time, being more significant in trimers derived from particular dimer conformation. The formation energy in some asphaltene and resin conformations is decreased compared to the asphaltene nanoaggregates with larger aromatic islands. Therefore, R rich in heteroatoms may be seen like an inner destabilizer naturally present in oil. These findings can guide new methods to control the stability of asphaltene aggregates by external chemical agents through the degradation mechanism directly upon the aliphatic chains.