Reducing the optical reflection of silicon (Si) material is a crucial issue on the surface of solar cells and other photonic applications. Fabrication of nanocone structures on the Si surface (black Si) by plasma (helium or argon) irradiation is a novel technique in recent decades with advantages, such as simple, economical, and harmless to the Si substrate. However, the uniformity and controllability of the surface remain problematic. In this study, uniform black silicon was obtained by low energy (<50 eV) helium ion irradiation with auxiliary Mo co-deposition. The characteristics of the nanocone show a clear relation with the Mo ratio. Deposited Mo was found to accumulate on the cone body, especially on the tip, and it worked as a nano mask to induce the formation of the nanocone and protect it from sputtering. The surface with high and large diameter nanocones possesses low reflectances of roughly 2%. The study of the relation between Mo ratio, characteristics of the nanostructure, and the reflectance of the surface raises a potential method of surface tailoring.