The paper contains results of quantum mechanical and molecular dynamics simulation of the structure, energy characteristics, and nanomechanical properties of nanoclusters of a “polymer matrix - carbon filler” composite medium. Quantum mechanical simulation is carried out in the framework of the cluster approach, in the approximation of microscopic friction and deformation (tension) for a model polymer - filler boundary layer. Molecular dynamics simulation is performed in NPT- and NVT-ensembles with periodic boundary conditions under normal conditions. Interaction parameters are determined according to the GROMACS force field, the potential energy of rotation about a bond is found from the quantum mechanical simulation results. The simulation findings are used to estimate strength properties of the medium. Based on the data of direct quantum mechanical calculation, we derive approximating dependences for potentials that describe interaction energy in the system “organic polymer matrix - carbon filler particles”. The molecular dynamics simulation data are used to calculate the compressibility factor.