Molecular dynamics (MD) simulations were conducted to investigate the interactions between a palygorskite coating and linear chain alkanes (dodecane C-12, tetradecane C-14, hexadecane C-16, and octadecane C-18), representing base oils in this study. The simulation models were built by placing the alkane molecules on the surface of the palygorskite coating. These systems were annealed and geometrically optimized to obtain the corresponding stable configurations, followed by the analysis of the structural changes occurring during the MD process. The interfacial interaction energies, mean square displacements, and self-diffusion coefficients of the systems were evaluated to characterize the interactions between base lubricant molecules and palygorskite coating. It was found that the alkanes exhibited self-arrangement ability after equilibrium. The interfacial interaction was attractive, and the electrostatic energy was the main component of the binding energy. The chain length of the linear alkanes had a significant impact on the intensity of the interfacial interactions and the molecular diffusion behavior. Moreover, the C-12 molecule exhibited higher self-diffusion coefficient values than C-14, C-16 and C-18. Therefore, it could be the best candidate to form an orderliness and stable lubricant film on the surface of the palygorskite coating. The present work provides new insight into the optimization of the structure and composition of coatings and lubricants, which will guide the experimental development of these systems for practical applications.