The stabilization of heavy oil plays an important role in the aggregation of asphaltene and resin molecules. Many experiments have been carried out to study the complex aggregation structures of asphaltene and resin molecules in heavy crude oils, but at the molecular level, these microstructures and properties are still unclear. As an auxiliary tool, molecular dynamics simulation can be used to simulate the behavior of asphaltene and resin molecules in heavy oil droplets or emulsified oil droplets. The simulation results show that (i) whether carboxylic acid asphaltene molecules or ordinary asphaltene molecules and resin molecules can form the netlike structure in heavy oil through face-to-face or side-to-side stacking interaction. (ii) When a surfactant molecules is added into heavy oil phase, ordinary asphaltene molecules move from the oil/water interface to the center of the emulsified oil droplet, but carboxylic acid asphaltene molecules are still at the oil/water interface. (iii) Molecular dynamics simulation shows that the emulsified oil drops at the hydrophilic interface, the hydrogen bond between the water molecules, and the relaxation time have a significant increase. Moreover, through the tensile simulation of the simulated system, the maximum force of the oil droplets formed by pulling apart the carboxylic acid asphaltene molecules is significantly smaller than that of the ordinary asphaltenes. When the sodium dodecyl sulfate molecule is added to the system, the maximum force of the oil droplets formed by pulling apart the ordinary asphaltene molecules is significantly reduced.