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For three-dimensional (3D) mono-layer molecular thin-film lubrication, the elasticity of the substrate affects the tribological behaviors of a thin fluid film confined by two solid substrates. To account for the elastic effects, this study establishes a multi-scale method that combines an atomistic description of the near region with a coarse-grained description of the far region of the solid substrate to simulate the thin-film lubrication. It is demonstrated that for a given temperature range and film–substrate coupling strength, the multi-scale method is in excellent agreement with the fully atomistic simulation. This study reveals that the elastic response of the substrate can be effectively rendered in the hybrid scheme. In the application of the multi-scale method to investigate the tribological properties of the multi-layer molecular thin-film lubrication, it is determined that the systematic static friction coefficient monotonously decreases as the molecular layer thickness in the fluid film increases. In comparison to the mono-layer molecular thin-film lubrication, the multi-layer molecular thin-film lubrication plays a role in reducing the friction and wear of the system.