The processes of diffusion-induced structure and phase formation in nanoscale Ni/Cu/V thin films deposited by DC magnetron sputtering on a Si (100) substrate after annealing in the temperature range of 200–550°С in vacuum (10$^{-3}$ Pa) and argon (200 Pa) atmospheres are studied. Thermal stability, diffusion mass transfer of components and changes of phase composition in vacuum and Ar atmospheres are analysed using synchrotron and copper radiation x-ray diffraction (XRD) and secondary ion mass spectrometry (SIMS). Due to the different diffusion mobility of Cu and Ni atoms with the temperatures increase in the studied interval, the two regions with different Ni and Cu concentrations are formed. Grain boundary and bulk mechanisms of Cu and Ni diffusion and the influence of the heat treatment atmosphere are discussed. As shown, annealing in vacuum atmosphere, compared to annealing in argon, results in an increase in the onset temperature of the Cu-based solid solution formation by 100°C and a decrease in the concentration of Ni in this solid solution. Thus, upon annealing in vacuum, the thin film maintains thermal stability over a larger temperature range compared with annealing in argon.