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To ensure the safe and economic operation of a waxy crude oil production process, the microdynamic mechanism and thermodynamic characteristics of the wax gelation process need to be revealed at nanoscale. The molecular dynamics model was established to characterize the phase transition and gelation behavior of waxy molecules in a multiphase system (including oil, asphaltene and water). The relative error between the simulated results and experimental data measured by Dutour et al. (2002) was 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 processes of dissolution, diffusion and aggregation. After which waxy cluster crystals with larger amount but smaller volume were formed, which would be deposited on the inner wall under the concentration gradient. The influence mechanisms of different operating parameters on wax gelation were analyzed. And it was found that the increase in temperature and water cut decrease the wax precipitation, while the increase in pressure enhance the wax precipitation rate. Furthermore, by means of hydrogen bonding and the effect of similar dissolution, water and asphaltene molecules also affect the wax precipitation process at the molecular scale. The investigations in this study provide theoretical support for the paraffin removal and control in a waxy crude oil production system. The molecular dynamics model and details. Image 1 • The MD model for characterizing the phase transition and gelation behavior of waxy molecules is established. • The microscopic mechanism of dissolution, diffusion and aggregation process of waxy crystals is revealed. • The influence mechanism of different operation parameters on phase transition and gelation process is studied. • We have confirmed that the hydrogen bond with the structure of C − H ⋯ O will form between water and waxy molecules. [ABSTRACT FROM AUTHOR]