The existing researches on interface properties between heterology materials mainly focus on semiconductor-metal and dielectric materials, but little on organic-inorganic ones. In recent years, the nanometer scale phenomena of interfaces between organic-inorganic is gaining a lot of attentions and becoming new frontier regions of nano-related research. Since gold exhibits excellent optical, electrical and mechanical properties, which can be applied to nano-optics, mechanics and electronics. Therefore this study aims to investigate the deformation behavior of nanaoindentation using molecular dynamics simulation and nanoindentation experiments. The nano-effect of mechanical properties between the interface of gold and heterologous Polymethyl Methacrylate (PMMA) with different side groups; i.e., Isotactic-PMMA, Syndiotactic-PMMA and Atactic-PMMA, are explored, respectively. The molecular structures of those side groups of the different PMMAs are identified and characterized. Those PMMA isomer thin films are prepared using spin-coater to deposit the different side groups of PMMA upon Au thin film. Sputter technique is used to form gold thin film with different thickness. The morphology on the surface of samples is characterized by using scanning electron microscopy (SEM) and X-ray diffraction (XRD). The indenter equipment is applied to realize the interface mechanical properties. The time-dependent properties of viscoelastic materials in nanoscale are measured using continuous stiffness measurement (CSM) nanoindentation technique. The effects of displacement rates on the hardness and modulus behavior of PMMA-based are investigated by nanoindentation. The mechanical properties are correlated with the side groups of the PMMA. The hardness of the PMMA-based increases with the raising displacement rate of the Berkovich tip. On the other hand, the modulus of the variation PMMA-based with the varied displacement rate of the Berkovich tip is not significant. The nanoindentation test shows different constituents in nanocomposite systems with a stronger material properties of the interface region than the matrix in each material.