Abstract: Sodium heat pipe is the key component for the heat transportation of the heat pipe cooled reactor. It’s very important to deeply understand the phase-change mechanism inside sodium heat pipe for its design and optimization. The phase change generally happens at the liquid-gas interface of the meniscus inside the wick pore of the sodium heat pipe. The thin liquid film of the meniscus is the main contributor to the heat transfer and resembles the whole boundary of the meniscus. In addition, the non-condensable gas (NCG) generally exists in the heat pipe. It also has effects on the phase change of thin liquid film. Due to the limits of thin liquid film’s nanoscale and high temperature conditions, it’s very difficult to study the thin liquid film by experiments or some traditional numerical methods. Molecular dynamics is always a powerful tool to explore some nanoscale phenomenons. It has been widely applied in the investigation of microscopic heat transfer. In this paper, the specific sodium heat pipe used in the PRHRS (passive residual heat removal system) of MSR (molten salt reactor) was chosen. Based on its start phase and normal operation, four cases were set (600, 700, 800 and 900 K respectively). Molecular dynamics software LAMMPS was adopted to simulate the equilibrium evaporation of thin liquid sodium film and liquid sodium was seen as the Lennard-Jones fluid. The mass accommodation coefficients (MACs) of four cases were obtained. Ar was used as the NCG and its effects were studied. The results show that the MACs of four cases are 0.388 6, 0.211 9, 0.261 5 and 0.241 6. When NCG exists, the values are 0.282 9, 0.254 3, 0.129 5 and 0.107 2. In the temperature range of initial startup and normal operation, NCG suppresses the phase change. In the last period of startup, NCG improves the phase change reversely. These effects coincide with many related macroscopic experiments. Based on the temperature and potential distribution inside the liquid film and vapor zone, the behind microscopic mechanism is revealed. NCG influences the phase change in two forms: it reduces the attraction between liquid atoms; it intensifies the interfacial reflection ratio of gas sodium atoms. This research could provide a new reference and theoretical support for the determination of the parameter of numerical simulation of the sodium heat pipe. It is the complement and extension for the macroscopic investigation of the sodium heat pipe. It is also the foundation for deep numerical simulation under the tendency of multi-scale couple computation.