The design of advanced nanostructured materials with predetermined physical properties requires knowledge of the relationship between these properties and the internal structure of the material at the nanoscale, as well as the dependence of the internal structure on the production (synthesis) parameters. This work is the first report of computer-aided analysis of high pressure consolidation (cold sintering) of bimetallic nanoparticles of two immiscible (Fe and Cu) metals using the embedded atom method (EAM). A detailed study of the effect of cold sintering parameters on the internal structure and properties of bulk Fe–Cu nanocomposites was conducted within the limitations of the numerical model. The variation of estimated density and bulk porosity as a function of Fe-to-Cu ratio and consolidation pressure was found in good agreement with the experimental data. For the first time, topological analysis using Minkowski functionals was applied to characterize the internal structure of a bimetallic nanocomposite. The dependence of topological invariants on input processing parameters was described for various components and structural phases. The model presented allows formalizing the relationship between the internal structure and properties of the studied nanocomposites. Based on the obtained topological invariants and Hadwiger’s theorem we propose a new tool for computer-aided design of bimetallic Fe–Cu nanocomposites.