Thermophoresis refers to the motion of small particles suspending in a fluid with non-uniform temperature distribution due to the temperature gradient around the particle. Usually, the fluid molecules coming from the hot side carry more kinetic energy than those from the cold side, which results in a net thermophoretic force in the direction opposite to the temperature gradient. Since it was discovered more than 100 years ago, thermophoresis has been of major importance in a variety of applications, where it can play either beneficial role or adverse role, including material synthesis, micro- and nano-fabrication, and environmental science. Therefore, it is necessary to accurately evaluate the thermophoretic force. In the present work, the thermophoretic force on nanoparticles is examined in the free molecule regime by using non-equilibrium molecule dynamics (MD) simulation. It has been widely accepted that the thermophoretic force conforms with the Waldmann equation for large Knudsen numbers. However, due to the effect of the nonrigid-body interactions between the particle and gas molecules, the thermophoretic force on nanoparticles might deviate greatly from the classical theory. In our MD model, a single nanoparticle with a diameter of several nanometers suspends in a diluted gas. The Lennard-Jones (L-J) potential is employed to simulate the intermolecular interactions. To avoid deforming the nanoparticle, the solid molecules within the nanoparticles are linked to their nearest neighbors through a finite extensible nonlinear elastic bonding potential. The thermophoretic force on a nanoparticle is calculated by imposing a harmonic potential on the nanoparticle, which eliminates the effect of the Brownian motion of the nanoparticle on the thermophoresis. The effective thermal conductivity of the ambient gas is employed in Waldmann equation for the thermophoretic force due to the finite volume effect. It is found that the Waldmann theory for thermophoresis is still valid for nanoparticles in the case of weak gas-particle interaction or high gas temperature. With the increase of the gas-particle interaction strength or the decrease of the gas temperature, the Waldmann theory is invalid due to the effect of gas-particle nonrigid-body collisions and the adsorption of gas molecules on the particle surface. By considering the gas-particle nonrigid-body interaction and the modified particle size, the theoretical results for thermophoretic force accord with the MD simulations quite well.