The molecular dynamics simulation model of nanoindentation is proposed in order to study the mechanical and structural deformation properties of an ultrathin MMA (methyl methacrylate) film on a Au(111) surface. First, the significant differences in the structural arrangement of MMA thin films with different thicknesses are observed. Two layers are apparent in the thinnest MMA thin film next to the Au(111) surface, while three layer structures are apparent in the thicker film. Second, this study examines the indentation tip that penetrates the MMA thin film into the An(111) substrate in order to understand the influence of the interface on the properties and deformation behavior in both the thin film and substrate. The result shows that the indentation force is influenced both by the layer structure and by the thickness of the MMA film. The thinnest case exhibits different deformation behavior from that of the thicker cases. In addition, the deformation of MMA molecules becomes significant at the interface between the MMA film and the Au(111) surface with the increase of film thickness, and detailed deformation behavior of the An surface for different thicknesses of MMA film is reported in this paper. Finally, both the rigid and the active models for the indentation tip are utilized in the simulation to examine the interaction differences between the tip and the film and the deformation mechanism.