The aggregates of asphaltene and resin molecules play an important role in stabilizing heavy crude oil. Although many experiments are applied to investigate the complex aggregating structure of asphaltene and resin molecules in heavy crude oil, those microstructure and properties are still not clear at the molecular level. As another auxiliary tool, molecular dynamics (MD) simulation can be used to simulate the behavior of asphaltene and resin in the heavy oil droplet or emulsified oil droplet. The simulation results showed the following: (i) Asphaltene and resin molecules can form a netlike structure in heavy oil through face-to-face or edge-to-face stacking interaction, and the aggregating structure is considered to be the main reason that heavy crude oil has high viscosity. (ii) When surfactant molecules were added to the heavy oil phase, the asphaltene molecules moved to the center of emulsified oil droplet from the oil/water interface. The adsorption of surfactant molecules at the interface resulted in an increase in the hydrophilic surface area of the oil droplet. We think that the changed hydrophilicity of emulsified oil droplet is the key to the viscosity reduction of heavy oil. (iii) The steered MD simulation can prove that the interaction among asphaltene and resin molecules becomes fragile in emulsified heavy oil droplet, and it indicates that the added surfactant molecules are beneficial to the viscosity reduction in crude oil.