Nickel was deposited on Si substrates and the feasibility of studying the formation process of Ni silicides with the atom‐probe mass spectrometer was examined by atomic layer‐by‐layer mass analysis of the specimen from the deposited layer to the substrate through the interface. The epitaxially grown silicide with a well ordered cubic structure was observed when the specimen was heated above 800 K. The main part of the Ni–Si mixed layer formed at room temperature was Ni‐rich Ni2Si regardless of substrate materials, Ni or Si. At high temperatures the Ni concentration in the mixed layer depends on the substrate materials. The result indicates that the silicide composition is regulated by the diffusivity of Ni into Si at low temperatures and by the relative quantities of Ni and Si at high temperatures. A clear interface between the silicide and the Si substrate was formed at around 800 K.