Nickel silicide has many advantages, such as low resistivity and low formation temperature; therefore, it has been widely used in the fields of solar cells, transistors and complementary metal-oxidesemiconductor (CMOS) devices. To obtain high-quality nickel-silicide thin film, solid-state reaction is a convenient and efficient fabrication method. For better understanding of the dynamic formation mechanism, we used in-situ transmission electron microscopy (TEM) to record the diffusion behavior during the heating process. In this work, three-steps annealing process to synthesize different nickel silicides corresponding to the various formation temperatures were investigated systematically. At 250 °C, the product of the first-step annealing was inverted-triangle Ni2Si, embedded in the Si substrate. Then, well-distributed NiSi thin film was synthesized, having the lowest resistivity among Ni-Si system at 400 °C. Finally, NiSi2, a Si-rich product, would form during the third-step annealing at 600 °C. NiSi2 product and Si substrate have small lattice mismatch; thus, the epitaxial relationship would be observed. We provide the evidence of diffusion behaviors and structural identification of Ni-Si system. Furthermore, these results are beneficial for the formation of specific nickel silicides, which is expected to optimize the fabrication of microelectronics.