A simple, practical method was developed to automatically align single crystalline Si nanocones (SiNCs) vertical to a Si substrate. Double heteroepitaxial structure of Si/CoSi2 on a Si (100) substrate was prepared by sputtering, and Si was then deposited on the surface via chemical vapor deposition with SiH2Cl2/H2 reaction gas. When Si was deposited at 900 °C, SiNCs were fabricated vertical to the substrate, had a tip curvature of about 100 nm, and had a number density of (0.9–35)×108/m2. A CoSi2 nanocrystal was clearly visible on the tip of each SiNC. These CoSi2 nanocrystals were formed by agglomeration of the Si/CoSi2 layer, and catalyzed the Si growth during chemical vapor deposition. In conclusion, the alignment of the fabricated SiNCs could be controlled by utilizing agglomeration in the Si/CoSi2/Si double heteroepitaxial structure.