The design and application of bitumen rheological property is an essential part of road engineering, which is strongly associated with colloidal structure form by millions of molecules. Our work aims at developing a transferable CGMD model for the bitumen molecular system to explore the microstructure in the Mesoscopic scale. In the present study, we focus on the mapping site construction and the validation of the modified MARTINI forcefield based on Flory-Huggins theory. On this basis, the CGMD model owned 126,692 molecules were built to research the influencing factors of bitumen aggregation, the dynamic evolution process of a three-dimensional periodic layer structure was observed. The result shows that the diffusion coefficient order of asphaltene, resin, oil, and model average is resin > model average > oil > asphaltene, and the order does not vary with temperature. At different character temperatures, the diffusion coefficients value has changed in orders of magnitude, which is correspond to viscoelasticity studies. Meanwhile, the molecular relative concentration at different temperatures has revealed the aggregation behavior of asphaltene in the bitumen, when the temperature is high enough, all the asphaltene molecules are separate to a certain distance and keep stable. With the temperature decreasing, some asphaltene molecules tend to move closer and form smaller aggregate.