Molecular dynamics provides a powerful tool to understand the elusive structureperformance relationship of asphalts. The combined molecular models were selected to investigate the interactions of the saturate, aromatic, resin, and asphaltene (SARA) four fractions and the correlation between fractions and the bee-like structures by atomic force microscopy in asphalts. The results showed that van der Waals was the main force to control intermolecular interactions. The arrangement of SARA fractions largely conformed to the modern colloid theory. However, some alkanes, sulfides, and condensed aromatics had different behaviors. Long-chain alkanes inserted into layers of asphaltenes, and small sulfides without long alkyl chains adhered to large sulfides or asphaltenes; nevertheless, counterpart condensed aromatics became much closer to those molecules. Strong interactions between the dispersed phase and continuous phase generated a larger size and greater number of bee structures. Asphaltenes played as a core, and long-chain paraffin played as an inducer, to affect the distribution of bee structures.