To address the issues of large volume change and low conductivity of silicon (Si) materials, carbon coatings have been widely employed as surface protection agent and conductive medium to encapsulate the Si materials, which can improve the electrochemical performance of Si-based electrodes. There has been a strong demand to gain a deeper understanding of the impact of efficient carbon coating over the lithiation and delithiation process of Si materials. Here, we report the first observation of the extended two-phase transformation of carbon-coated Si nanoparticles (Si/C) during electrochemical processes. The Si/C nanoparticles were prepared by sintering Si nanoparticles with polyvinylidene chloride precursor. The Si/C electrode underwent a two-phase transition during the first 20 cycles at 0.2 C, but started to engage in solid solution reaction when the ordered compact carbon coating began to crack. Under higher current density conditions, the electrode was also found to be involved in solid solution reaction, which, however, was due to the overwhelming demand of kinetic property rather than the breaking of the carbon coating. In comparison, the Si/C composites prepared with sucrose possessed more disordered and porous carbon structures, and presented solid solution reaction throughout the entire cycling process.