In order to ensure the safe and economic operation of waxy crude oil transportation process, the micro-dynamic mechanism and thermodynamic characteristics of wax precipitation process at nanoscale are necessary to be revealed. Here, we established the molecular dynamics model to characterize the phase transition and precipitation behavior of waxy molecules in multiphase system (including oil, asphaltene and water), the relative error between simulated results and experimental data measured by Dutour et al. (2002) is less than 5%. Under the coupling effect of different operation parameters, the molecular dynamics simulation was employed, the simulated results showed that the spherical paraffin crystals underwent the process of dissolution, diffusion and aggregation, then the waxy cluster crystals with larger amount but smaller volume would form, and it would deposit on the outer wall under the concentration gradient. The influence mechanism of different operating parameters on wax precipitation was analyzed, of which the increase of temperature and water cut will decrease the wax precipitation, while the increase of pressure will enhance the wax precipitation rate, furthermore, by means of the hydrogen bonding and the effect of similar dissolution, the water and asphaltene molecules also affect the wax precipitation process at molecular-scale. The researches of this paper provide the theoretical support for the paraffin removal and control in waxy crude oil pipeline transportation process.