Transport properties of nanoparticles in gases have many practical applications, such as aerosol science, combustion, and micro- and nano-scale fabrication. A nanoparticle moving in a fluid is expected to experience a drag force, which determines the transport property of the particle. According to the Einstein relationship, the diffusion coefficient of a particle is inversely proportional to the drag force coefficient. However, in the transition regime, it is usually difficult to evaluate the drag force of suspended particles. A typical method is to extend the asymptotic solution of the free molecular or continuum limit to the transition regime. According to the gas kinetic theory, Li and Wang proposed a theoretical expression for drag force on nanoparticles in the free molecular regime, which is then extended to the entire range of Knudsen number following a semi-empirical approach Li Z G, Wang H 2003 Phys. Rev. E 68 061207. For nanoparticles, it is necessary to verify the theoretical predictions since the gas-particle non-rigid-body interactions must be taken into account. In this work, the drag force on nanoparticle in the transition regime is investigated by using molecular dynamics (MD) simulation. To evaluate the drag force, a harmonic potential is used to the nanoparticle to constrain its Brownian motion in our MD simulation. In the steady state, the drag force can be obtained by the balance between the drag force and harmonic force. It is found that the gas-particle non-rigid-body interaction has a significant influence on the drag force of nanoparticle. For weak gas-solid coupling, the MD simulation results can be in good agreement with the prediction of Li-Wang theory. However, for strong coupling, there exists significant discrepancy between the MD simulation results and the theoretical results. Due to the gas-solid intermolecular interactions, gas molecules can be adsorbed on the nanoparticle surface, and after a time period, they may be re-emitted from the surface when they gain sufficient kinetic energy. Therefore, an adsorption-desorption equilibrium and an adsorption layer can be established on the particle surface. The adsorption layer enlarges the collision cross-sectional area and enhances the momentum transfer between gas molecules and the particle, and thus the drag force increases. This can explain the inconsistencies between the theoretical results and MD simulations. In this work, we introduce an adsorption ratio to evaluate the thickness of the adsorption layer. Then, the effective particle radius can be defined by the sum of particle radius and the thickness of the adsorption layer. By using the effective particle radius, the simulation values are in very good agreement with the theoretical predictions. The results of this work provide insights into the applications of nanoparticles in aerosol science.