The paper considers the modeling of a multilayer nanocomposite, the combination of elements of which gives rise to a spin valve effect. The relevance and importance of effects in the field of spintronics and related materials and devices are described. We study the composition and atomic structure of individual layers of a multilayer nanocomposite, as well as the composition and morphology of the interface of nanocomposite layers. We analyzed a sample with a periodic superconductor-ferromagnet structure consisting of more than 20 alternating layers of niobi-um and cobalt. The deposition process took place in a deep vacuum. The simulation was carried out by the molecular dynamics method using the potential of the modified immersed atom meth-od. The formation of layers was carried out in a stationary mode. The temperature was adjusted using the Nose-Hoover thermostat. The deposition of each nanofilm ended with a relaxation stage for the necessary stabilization and restructuring of the formed nanocomposite. Three deposition temperature regimes were considered: 300 K, 500 K, and 800 K. For these modes, we analysed the atomic structure of nanofilms and transition regions (interface) formed between the layers. A study of the atomic structure of nanofilms showed that niobium is formed by crystalline regions of different orientations. A cobalt nanofilm is characterized by a structure close to amor-phous. The structural features of the interface between the superconductor-ferromagnet layers largely depend on a relief of the surface onto which the deposition is made. The smallest varia-tion in atomic composition is observed in the first niobium-cobalt contact zone, since the formation of the first nanofilm occurs on an even plane of the substrate. An analysis of the influence of the temperature regime during the formation of the nanosystem shows the dependence of the processes of formation of multilayer nanofilm formation, the interface of nanolayers, as well as the composition and morphology of heterostructures on the temperature at which a nanocomposite is manufactured. An increased temperature leads to the formation of a more rarefied structure of nanolayers and an increase in the zones of the interface of nanolayers due to the diffusion of atoms of the sprayed materials.