Graphene and fullerene nanoparticles exhibit remarkable tribological performance in solid–liquid composite lubrication systems. However, the atomic-scale understanding of how surface topography influences tribological behavior and performance is still limited. Herein, the mechanisms by which surface topography features (achieved by regulating the asperity amplitude and frequency parameters) influence system lubrication performance and nanoparticle friction behavior were systematically investigated through friction experiments and molecular simulations. The results indicate that at the micro-nanoscale, the amplitude parameter predominantly governs the surface roughness features and frictional resistance. This is because an increased amplitude strengthens the boundary lubrication effect, exacerbates the stress concentration and structural deformation of graphene, and makes fullerene prone to filling grooves but less capable of bearing normal loads, thereby exacerbating friction and wear (friction coefficient increased by 59%). In contrast, the frequency parameter primarily determines the surface kurtosis features and normal force. At low frequencies, low kurtosis features intensify the normal squeezing effect of asperities, inducing the hydrodynamic pressure effect of the base oil, thus enhancing lubrication performance (friction coefficient decreased by 22%). Compared with frequency, the pronounced influence of amplitude on the lubrication state and interface contact behavior dominates the tribological properties of the system and the lubrication mechanism of the nanoparticles. Low surface roughness and kurtosis features are critical for achieving efficient lubrication. This study offers valuable insights into the design of surface topography and the optimization of lubrication performance.