Abstract In this study a novel mesh algorithm is introduced to investigate the elastic properties of Polymer Nano-composite (PNC) materials based on the scaled boundary finite element method (SBFEM). The proposed procedure is applied efficiently with very simple mesh and few degrees of freedom compared to the classical finite element method. First, the nanoparticles are randomly distributed within the epoxy matrix to numerically shape the geometry of composite material. Second, a flexible sub-structuring technique in accordance with the random distribution is utilized to model the variation in material and geometry. Next, The interphase of nanoparticles is integrated properly by the new sub-domains generated from the algorithm. Finally, the elastic properties of the material are estimated. The result based on SBFEM showed full agreement with FEM predictions and the corresponding experimental measurements obtained from the literature.