Here we summarize the current main progress achieved in the aspect of rubber nanocomposites studied through molecular dynamics simulation, including the dispersion mechanism of nanofillers with various geometrical shapes in rubbery chains, the interfacial interaction between fillers and rubbery chains(whether the glassy polymer layer exists), the strengthened mechanism of the stress-strain behavior, the adjusting of the visco-elasticity of rubbery chains by the introduced carbon nano-springs and the mechanism accounting for the non-linear behavior of rubber nanocomposites. Elucidating these basic questions will provide significant scientific basis and theoretical guidance for preparing rubber nanocomposites with both excellent static and dynamic mechanical properties, further promoting the development of Chinese green automobile tires with high performance. Lastly, we briefly evaluate the challenges with regards to the structure-property relation of rubber nanocomposites investigated through computer simulation. Keywords: rubber; nano-reinforcement; dispersion; interface; static and dynamic mechanics; molecular dynamics simulation