Nanostructuring is an effective strategy to enhance the structural and cycling stability of silicon anodes in lithium-ion batteries. However, a controllable and cost-effective method for synthesizing nanostructured silicon with various morphology is still a challenge. Herein, we synthesize zero-dimensional, two-dimensional, and three-dimensional silicon nanostructures directly using low-cost and abundant clay minerals as precursors without any pretreatment and templates. Our results show that the morphology and microstructure of the resulting nanostructured silicon strongly depend on the architectural features of clay minerals, i.e., zero-dimensional silicon from palygorskite, two-dimensional silicon from montmorillonite, and three-dimensional silicon from halloysite. The silicon nanostructures show large specific surface area (over 80 m2 g−1) and hierarchical pore structure. As anodes in lithium-ion batteries, two-dimensional nanostructured silicon from montmorillonite exhibits the best electrochemical performance (i.e., 1369 mAh g−1 at 1.0 A g−1 with a capacity retention of 78% over 200 cycles). This work provides a universal guideline from clay minerals to various silicon nanostructures via an economical and scalable strategy, and reveals the fundamental structure-property relationship of different silicon nanostructures synthesized under the same condition, which would contribute to the large-scale production of high-performance and low-cost silicon-based anodes in lithium-ion batteries.