Ni silicide synthesis by Ni ion beam irradiation into Si attracts attention due to its advantages including the ability of formation of local structures, the controllability of ion beams, the formability of silicide without heat treatment and the high reproducibility of the resulting specimen. In this work, we investigate the local atomic structure of Si implanted with 3.0 MeV Ni+ ions. Analysis of Ni K-edge fluorescent-yield extended X-ray absorption fine structure reveals that Ni atoms have mixed structure of metallic-like face-centered cubic Ni and NiSi2 phases at the initial stage of the irradiation and the formation of NiSi2 promotes significantly with the ion fluence above 1015 ions⋅cm−2. With consideration of the agreement between the ion fluence threshold for the structural transition and the critical Si-amorphization fluence (7.1 × 1014 ions⋅cm−2), it is concluded that the amorphization of Si plays an important role in the synthesis of the NiSi2 phase in Ni+-irradiated Si.