Rational design of silicon and carbon nanocomposite with a special topological feature has been demonstrated to be a feasible way for mitigating the capacity fading associated with the large volume change of silicon anode in lithium ion batteries. Although the lithiation behavior of silicon and carbon as individual components has been well understood, lithium ion transport behavior across a network of silicon and carbon is still lacking. In this paper, we probe the lithiation behavior of silicon nanoparticles attached to and embedded in a carbon nanofiber using in situ TEM and continuum mechanical calculation. We found that aggregated silicon nanoparticles show contact flattening upon initial lithiation, which is characteristically analogous to the classic sintering of powder particles by a neck-growth mechanism. As compared with the surface-attached silicon particles, particles embedded in the carbon matrix show delayed lithiation. Depending on the strength of the carbon matrix, lithiation of the embedded silicon nanoparticles can lead to the fracture of the carbon fiber. These observations provide insights on lithium ion transport in the network-structured composite of silicon and carbon and ultimately provide fundamental guidance for mitigating the failure of batteries due to the large volume change of silicon anodes.