This study is focused on evaluating the aggregation behavior of four asphaltene molecules (PA3-type) dissolved in three different solvents. Hence, solution models composed of asphaltenes dissolved in toluene, n-heptane, and mixtures of n-heptane and toluene (known as heptol), were evaluated with molecular dynamics (MD) simulations. For MD calculations, four PA3-type structures were chosen to evaluate the effect of the location of one heteroatom in the polyaromatic core on the aggregation behavior. The first structure consists of only a CH structure, the second has sulfur, the third has nitrogen, and the last one contains oxygen. The heteroatom was replaced in the same location in one of the five-membered rings in the center of the molecule to test the different chemical effects induced by these heteroatoms. Molecules with the heteroatoms showed a higher aggregation tendency in n-heptane than in heptol-50 and toluene, with an average size of 12.8, 6.2, and 2.4 molecules per aggregate, respectively, whereas the PA3 molecule with no heteroatom forms less and smaller aggregates. The inclusion of only one heteroatom increases the polarity and the planarity of the molecule, increasing the attractive interaction energies (140−160% in n-heptane) and the overall aggregation tendency. The molecule with the sulfur heteroatom forms bigger and more stable aggregates than molecules with oxygen and nitrogen. In conclusion, the inclusion of heteroatoms in the PA3 structure increases the polarity and planarity of the molecule, improving the aggregation tendency in all solvents, notoriously in n-heptane.