In this work, we have studied the structure evolution of Ni/Ti layered stacks with a modulation period of 30 nm and 15 nm (total thickness of the stack is of 60 nm) deposited by RF magnetron sputtering onto $p$-Si (001) substrate upon vacuum annealing up to 700°C. As found based on the XRD, SIMS and four-point probe resistivity measurements’ data, the diffusion-induced reactions in both stacks occur through the stages of metals’ intermixing, amorphization and formation of intermetallic Ni$_{x}$Ti phases. The application of a smaller modulation period leads to the more intense metals’ intermixing, which results in the shift of the structural transitions onset to the lower temperatures. However, the modulation period does not influence the temperature range of amorphization, which is of $\cong$ 38°C for both stacks.