Abstract: The thermophoresis of water droplets in carbon nanotubes is studied by using molecular dynamics (MD) simulations. Owing to the temperature gradient in the carbon nanotubes, the water droplets can move along the axial direction from high to low temperature. However, it is difficulty to calculate the thermophoretic forces on water droplets in carbon nanotubes owing to the Brownian motion of water droplets, and the mechanism of thermophoresis still unclear. In this paper, by imposing a harmonic force to the water droplet, the thermophoretic force acting on the water droplet can be obtained based on the balance between the thermophoretic force and the harmonic force. The results indicate that as the number of water molecules of the water droplets increases, the interaction energy between the water droplets and carbon nanotubes gradually strengthens, and the thermophoretic force increases. As the diameter of carbon nanotubes gradually increases, the thermophoretic force also increases due to the increase in the number of water molecules per unit area. As the system temperature increases, water molecules are more likely to overcome the potential barrier at the solid-liquid interface and detach from the interface, leading to enhanced interfacial hydrophobicity and a corresponding reduction in the thermophoretic effect. In addition, applying an external axial electric field to the system, as the electric field strength increases the thermophoretic effect significantly enhances, and the direction of the dipole vectors of the water molecules gradually be the same as the direction of electric field. This paper reveals the thermophoresis mechanism of water droplets in the carbon nanotubes, which helps to understand the thermophoresis phenomenon at the solid-liquid interface in nano-confined structures.