The challenges faced by the oil and shale industries include the comprehension of the physical chemical behavior of heavy-weight phases. These phases have a high tendency to aggregate, mainly as a result of the presence of asphaltenes, the composition of which has been fairly unclear up to now. The chemical composition of this phase is one of the driving forces behind the physical chemical behavior in oil, and the structure property relations of these systems are key in the development of improved refining techniques, including the design of new catalysts. In this paper, the aggregation of asphaltene molecules is studied with regard to molecular architecture and variations in the size of the aromatic core and lateral chain length using classical molecular dynamics simulations. How these characteristics are impacted by the temperature and pressure is also examined. This analysis provides a general overview of the factors that have the strongest impact on the formation and stability of nanoaggregates and clusters of nanoaggregates.