Though silicon (Si) is expected as a high capacity negative electrode for lithium-ion batteries, its drastic structure change during lithiation/delithiation cycling hampers its stable cyclability. In this work, we report that a specific structure, a wrinkled structure, is temporarily formed from Si nanoparticles (particle size was ca. 82 nm) at relatively early numbers of lithiation/delithiation cycling, and that the wrinkled structure thus formed shows a good performance. Though this structure soon transforms into a different one, resulting in fading of the performance, such transformation of the Si framework can be frozen at the state of the wrinkled structure by restricting lithiation degree. Interestingly, when Si nanoparticles are covered with a carbon nanolayer (thickness was ca. 10 nm) beforehand, the carbon layer is also deformed together with Si and is taken in by the wrinkled structure. Such carbon-coating improves the rate performance of Si nanoparticles; the carbon-coated Si nanoparticles show a constant discharge capacity of 1500 mAh g−1-composite over 100 cycles and exhibit an excellent rate performance (1500 mAh g−1-composite even at a rate of 3.3 C).