As a representative specimen of the MST in liquid, we performed the above simulations for polystyrene nanoparticles (PSNPs) with a diameter of 500 nm in water. As a result, the NPs moved away from the heating spot over time. To verify the computational model, experiments were performed using equivalent samples and heating conditions, and satisfactory agreement was obtained between the experimental and numerical results in the behavior of thermophoretic depletion from the heating spot; this demonstrated that it is possible to quantitatively evaluate the thermophoretic force acting on nanoparticles. Because all the files for numerical calculations used in this article, including COMSOL files and Python codes for the BDS, were uploaded in Supporting Information, anyone can perform these simulations. The computational method in this paper will be useful in making effective predictions and quantitatively evaluating and interpreting experimental results in the course of experimental research on thermophoresis.