The molecular dynamics model was established to characterize the homogeneous and heterogeneous nucleation processes for a waxy crude oil multiphase system at the nanoscale. Using the established model, the homogeneous and heterogeneous nucleation processes were numerically simulated, and the accuracy of the model was verified by comparing the simulation results with those of classic nucleation theory. On this basis, the micromechanism for the effect of different cooling rates on the nucleation process was studied, and it was determined that the homogeneous and heterogeneous nucleation would coexist and compete with each other in the initial stage and, at last, a large spherical cluster would form. Furthermore, the calculation model for the interfacial free energy was proposed, the interfacial free energy with nucleation centers of different specific area factors were numerically calculated, and the influence rules of the interface effects on the nucleation process were clarified. Besides, the heterogeneous nucleation process of different nucleation center materials was simulated, and the aggregation degree and element composition of nucleation clusters were analyzed. Finally, the influence mechanism of doping ions on the nucleation process was investigated. The investigations in this study provided a theoretical basis for ensuring a safe and economic operation of waxy crude oil production.