Micro- or nano-structuring is essential in order to use Si as an anode material for lithium ion batteries. In the present study, we attempted to use Si wafers with a spiky microstructure (SMS), the so-called black-Si, prepared by a cryogenic reactive ion etching process with an SF6/O2 gas mixture, for Li half-cells. The SMS with various sizes of spikes from 2.0 μm (height) × 0.2 μm (width) to 21 μm × 1.0 μm was etched by varying the SF6/O2 gas flow ratio. An anode of SMS of 11 μm-height in average showed stable charge/discharge capacity and Coulombic efficiency higher than 99% for more than 300 cycles, causing no destruction to any part of the Si wafer. The spiky structure turned columnar after cycles, suggesting graded lithiation levels along the length. The present results suggest a strategy to utilize a wafer-based Si material for an anode of a lithium ion battery durable against repetitive lithiation/delithiation cycles.