In this study, bilayer thin films with different layers’ order, Ni/Ti/Si (100) and Ti/Ni/Si (100), are prepared by magnetron sputtering at room temperature followed by the thermal annealing in a vacuum in the temperature range from 400°C to 600°C for 1 h. The combination of XRD and SIMS techniques is used to investigate the effect of the layers’ inverse arrangement on the crystalline structure, phase formation and elemental composition upon thermal treatment. As revealed, the annealing of the Ni/Ti bilayer leads to the diffusion of Ti atoms through the Ni grain boundaries towards the outer surface. For the case of Ti/Ni bilayer, interdiffusion between Ni and Ti is not detected upon heat treatment, whereas the thermally induced diffusion between Ni and substrate resulted in the formation of NiSi silicides is revealed. The likely structural and thermodynamic reasons for such behaviour are discussed.