Thermal stability of polycrystalline NiSi2 on high‐dose BF+2‐, Si+‐, B+‐, F+‐, As+‐, and P+‐implanted (001) Si has been studied by both cross‐sectional and plan‐view transmission electron microscopy as well as by sheet resistance measurements. The surface coverage and grain size of polycrystalline NiSi2 were found to be significantly influenced by the implantation species in silicon substrate. In Si+‐, B+‐, As+‐, and P+‐implanted samples, agglomeration of NiSi2 became very severe after 800 °C, 1‐h annealing. The average grain sizes were larger than 0.5 μm. In contrast, almost full surface coverage was found in F+‐ and BF+2‐implanted samples after 900 °C, 1‐h annealing. The growth of laterally uniform NiSi2 and resistance to agglomeration at high temperatures in BF+2‐ and F+‐implanted samples are attributed to the retardation of the growth of NiSi2 grains by the presence of fluorine bubbles at the grain boundaries. Sheet resistance data were found to correlate well with the morphological and microstructural observation.