The finite element method (FEM) is an essential tool for exploring the complex behaviors of advanced materials and nanocomposites, particularly when experimental analysis is challenging. This study refines the modeling of graphene-reinforced nanocomposites by developing and validating 3D representative volume elements (RVEs) using FEM. The RVE geometry is designed with an embedded-like structure, which optimizes load distribution and enhances mechanical performance. In these models, graphene is simulated as surface geometry with shell elements, while the matrix and interphase regions are represented as 3D continua, with the interphase modeled at the theoretical thickness of graphene. This approach significantly improves the accuracy of mechanical property predictions by enhancing load transfer mechanisms and minimizing assumptions. The 3D RVE models were validated against other numerical data and employed to predict key elastic properties, including elastic and shear moduli, across various graphene volume fractions and sizes. Additionally, linear dynamic simulations were conducted to investigate the material’s vibrational characteristics, offering deeper insights into the mechanical performance of the nanocomposites. The results suggest that this modeling approach could be particularly beneficial for applications in industries requiring high-performance materials, such as aerospace and automotive sectors.