A high-capacity and high-rate-capability anode material for lithium-ion batteries, silicon-doped iron oxyhydroxide or 2-line ferrihydrite (2Fh), was prepared by mixing iron nitrate powder, tetraethyl orthosilicate, 2-propanol, and ammonium hydrogen carbonate powder at room temperature. The design of this material was inspired by a bacteriogenic product, a nanometric amorphous iron-based oxide material containing small amounts of structural Si. The atomistic structure of the prepared Si-doped 2Fh was strongly affected by the Si molar ratio [x = Si/(Fe + Si)]. Its crystallinity gradually decreased as the Si molar ratio increased, with a structural variation from nanocrystalline to amorphous at x = 0.25. The sample with x = 0.20 demonstrated the best Li storage performance. The developed material exhibited a high capacity of ∼400 mAh g−1 at the 25th cycle in the voltage range of 0.3–3.0 V and at a current rate of 9 A g−1, which was three times greater than that of the Si-free 2Fh. This indicates that Si-doping into the 2Fh structure realizes good rate capability, which are presumably because of the specific nanocomposite structure of iron-based electrochemical centers embedded in the Si-based amorphous matrix, generated by reversible Li insertion/deinsertion process.