Silicon-based materials are one of the most promising anode materials for lithium-ion batteries (LIBs) because of their theoretical capacity which is ten times higher than that of conventional graphite. However, the complex fabrication process and the high cost of silicon-based nanomaterials limit their practical application. In this study, equisetum fluviatile was used as raw material to prepare a three-dimensional porous biogenic Si/C composite (3D-bio-Si/C) by deep reduction, mild oxidation and carbon coating processes. The three-dimensional porous structure not only allows rapid diffusion of Li⁺, but also provides enough voids to accommodate the volume change on Li⁺ insertion and extraction. Benefiting from the abundant internal porosity and the high-strength outer carbon film of the three-dimensional porous structure, the obtained 3D-bio-Si/C shows remarkable electrochemical performance. This 3D-bio-Si/C can deliver reversible specific capacity of 1243.2 mAh/g at a current density of 1 A/g, and maintain 933.4 mAh/g after 400 cycles. This low-cost, scalable, green and sustainable route to synthesize high-performance silicon-based anode material derived from equisetum fluviatile lays a foundation for the commercial preparation of Si based lithium-ion battery anode materials.