Silicon nanowires (SiNWs) have attracted attention as promising high efficiency thermoelectric materials by significantly improving the thermoelectric efficiency of silicon. Here, we have fabricated cobalt silicide/silicon heterostructure on both ends of nanowires using self-aligned silicide (salicide) process. By forming cobalt silicide (CoSi2) layer on SiNWs, the thermal conductivity of SiNWs with diameters of 200, 350, and 500 nm decrease to 25.1, 31.3, and 38.1 W·m−1·K−1, respectively, which is about 8% reduction on average. Since the phonon nanoinclusion scattering is influenced by the density of the nanoinclusions, the thermal conductivity tends to decrease as the volume fraction of CoSi2 in SiNWs increases. The Seebeck coefficient of the heterostructured nanowires increases to 255 μV/K, which is mainly attributed to the low-energy charge carrier filtering effect due to the Schottky barrier at the CoSi2/Si interfaces. The measurements show that the figure-of-merit ZT of the heterostructured nanowires is improved by 10% on average compared with the conventional SiNWs. Consequently, the CoSi2/Si heterostructured nanowires enhance the thermoelectric properties of SiNWs effectively by suppressing phonon transport and improving electron flow.