The formation of multilayer nanosystems for spintronics is a complex technological process during which it is necessary to obtain a complex composition from various materials. The selection of technological parameters providing a necessary atomic or molecular structure of the individual layers of the nanosystem requires quite lengthy and expensive experiments. It should also be noted that along with the physical parameters of the nanosystem, it is necessary to ensure its stability in time and operational reliability. Given the above, it is possible to note the prospects of mathematical modeling to accelerate research and a detailed understanding of these problems. The report is devoted to the study of formation processes of multilayer nanostructures for spintronics. The study was carried out by the method of mathematical modeling. The behavior of the multilayer nanosystem was described by the method of molecular dynamics. A modified immersed atom method was used as a potential. To maintain a constant temperature in the nanosystem, a Nose – Hoover thermostat was used. Demonstrated theoretical approaches to the study of the processes of formation and deformation of such type nanosystems. The simulation allowed us to establish the basic laws of changes in the atomic structure of the different layers of nanosystems. The results of theoretical studies processes of formation of multilayer nanostructures for spintronics can be used in the development of technological in industry.