We have investigated effects of carbon pre-implantation (C-implantation) on electrical and morphological properties of nickel silicide (NiSi). C-implanted NiSi showed an improved thermal stability on the electrical characteristics in terms of sheet resistance (Rsh) and contact resistivity (ρc) after rapid thermal annealing (RTA) up to 700 °C. The process temperature window was extended by ~100 °C when the C-implantation with a dose of 1 × 1015 cm−2 was introduced. From transmission electron microscopy (TEM) images, the suppression of NiSi agglomeration was confirmed in the C-implanted NiSi. In order to further understand the role of carbon, atom probe tomography (APT) was performed. The three-dimensional (3D) distribution and composition of elements by APT unveiled the formation of carbon clusters with a diameter ranging from 2 to 10 nm near the NiSi/Si interface. The carbon clusters with a peak concentration of 6.0 at. % at the NiSi/Si interface can effectively suppress NiSi agglomeration and Ni diffusion, resulting in improving thermal stability of the NiSi.