Simulation of molecular dynamics (MD) allows mimicking the systematic variation of mechanical properties beyond the capacity of experimental methods. In this review, the status of the molecular modelling, simulation and mechanical and thermal characterisation of graphene and the properties of bulk nanocomposites using MD are extensively examined. The molecular models of graphene (pristine and functionalised), and the most common epoxy matrix with preeminent MD energy minimisation tools are thoroughly examined. The presence of MD’s simulation setup and the computational procedure for different styles of mixing the polymer matrix with graphene as nanofiller are exhaustively reviewed. In particular, in the analysis of several papers on graphene and their composites, it has been noticed that mechanical, thermal and interfacial properties are ubiquitous to most of the engineering applications. In this review, advances in the molecular modelling and simulation of graphene and their composites has been discussed in detail keeping graphene structures, aspect ratio, weight fraction and density effect as major factors. Finally, the research gaps and future scope are discussed, which indeed helps the researchers in scaling up their researches in graphene and their composites, which may further lead to their experimental findings.