Composites consisting of polymer matrix and nano-sized carbon-silica filler (mineral schungite’s components), their energy and strength characteristics were the topics of the presented paper. The aim of the study was to investigate the structural and mechanical properties of above composites in the framework of quantum chemical approach, to create the scientific basis of composite strengthening and to investigate the possibility and prospects of mineral nanosize fillers application for preparing composites with enhanced mechanical properties. The microscopic structure and mechanical properties of the composite components and adsorption complexes of those with polymer matrix, as well as the interphase layer between the composite components were studied the course of the modeling. We applied the coordinate of the microscopic deformation and the cluster approaches. Calculations were carried out in parallel mode. Microscopic mechanisms that determine the deformation and interface friction in the polymer composites based on carbon-silica filler were proposed in our study. It was shown how the structure and surface modification of composite components impact on their structure and deformation properties. Thus the method of computer-aided component selection of nanofilled composites with improved strength characteristics was proposed.