Asphaltene is the heaviest and most polar component of the crude oil. Asphaltene precipitation and deposition results in some adverse processes in both upstream and downstream petroleum industry such as formation of water-in-oil emulsions, wettability alteration of the reservoir rock, pore blockage leading to permeability impairment, blockage of transportation pipeline, and catalyst poisoning in refineries. Asphaltene self-aggregation plays a major role in all these operational difficulties. Although several studies have been carried out on asphaltene aggregation, there is limited scientific understanding of asphaltene self-aggregation at the microscopic level. In this study, Quinolin-65 molecule is considered as a model asphaltene structure. The effect of various factors contributing to self-aggregation of Quinolin-65 molecules including intermolecular interactions, temperature, pressure, solvent, and molecular structure are investigated using quantum mechanics analysis and molecular dynamics (MD) simulations. Results of reduced density gradient (RDG) analysis demonstrated that the strong van der Waals interaction between aromatic rings in two Quinolin-65 molecules is a critical factor in their dimerization and self-aggregation. Radial distribution function, potential of mean force, and mean square displacement are calculated using MD simulation. The Quinolin-65 aggregation tendency in the toluene medium is significantly decreased compared to that in the water and heptane media, due to the interactions between the Quinolin-65 molecules and toluene. According to the MD simulation results, the solubility parameter of the medium can affect the Quinolin-65 aggregation process. The stability of Quinolin-65 molecule in the medium is increased by increasing the temperature. Upon a change in the Quinolin-65 aggregation behavior, the free energy variation range with pressure and temperature is from −4.01 to −0.23 kjmol and −3.49 to −0.56 kjmol, respectively. This study provides new insights/findings to better understand the interaction force(s) between the Quinolin-65 molecules as well as the effect of different thermodynamic conditions on Quinolin-65 molecules self-aggregation at the molecular level. Moreover, this research work assesses the synergistic effects of influential parameters (e.g., thermodynamic conditions, solvent, and structure) on the Quinolin-65 self-aggregation behavior, which can help predict some serious flow assurance issues associated with the precipitation/deposition of asphaltene particles.