Interfacial reactions of nickel thin films on BF+2‐implanted (001)Si annealed at 200–900 °C for various periods of time have been studied by both cross‐sectional and plan‐view transmission electron microscopy as well as by sheet resistance measurement. Drastic difference in NiSi2 formation was found between samples with implanted amorphous and regrown substrates. In samples with implanted amorphous substrates, polycrystalline NiSi2 was found to be the stable phase after annealing at 400–900 °C. In contrast, although epitaxial NiSi2 was formed on implanted regrown samples at a temperature as low as 250 °C, the dominant phase was NiSi in samples annealed at 400–700 °C. The presence of B and/or F atoms in silicon was found to be essential for the formation of epitaxial NiSi2 on crystalline silicon at low temperatures. The final structure of the silicide layer was found to depend critically on the thickness of starting Ni overlayer and the annealing temperature. In addition, the amorphicity of the substrate apparently played an important role in promoting the formation of polycrystalline NiSi2 at low temperatures. From a comparison with Si+ implanted amorphous samples, the growth of laterally uniform NiSi2 and resistance to islanding at high temperature in BF+2‐implanted amorphous samples are attributed to the retardation of the growth of NiSi2 grains by the presence of B and/or F atoms at the grain boundaries. Sheet resistance data were found to correlate well with the microstructures of the systems.