One of the causes of capacity fading in cells containing silicon anodes is the growth of a secondary SEI. A possible way of solving this problem is to create an anode with a highly porous three-dimensional structure, in which the growing SEI could be accommodated without blocking conduction pathways inside the anode. We evaluated this approach by building a 3D carbon-fiber (CF) scaffold matrix made by the pyrolysis of cotton wool. Anodes fabricated from bare and carbon-coated silicon nanoparticles, were studied from the viewpoint of the influence of anode structure and LixSi phase transformations on prolonged cycling of Li/Si cells. Analysis of the mechanisms of degradation of silicon anodes in lithium-ion batteries provides possible ways of elimination of the negative effect of the growth of the SEI on capacity fading. It will be noted that all the anodes containing cotton carbon fiber matrix exhibit much more stable cycle life than do CF-free anodes. The synthesis of the carbon-fiber (CF) scaffold matrix is simple and easy to scale up to industrial production.