We prepared nano-sized Si clusters dispersed uniformly in carbon-coated SiO (C-Si/SiO) and thoroughly investigated the morphology of the solid electrolyte interface (SEI) formed on the C-Si/SiO electrodes before and after a charge-discharge cycling test. The 30 cycles at 1000 mAh/g (deep) showed an excellent durability compared to those at 500 mAh/g (shallow). The different SEIs with the crack-contained and smooth electrode surfaces were formed after the deep and shallow cycles, respectively. Their SEI components which originated from hydrocarbons, Li alkyl carbonate, Li2CO3, LiF, and phosphorus oxide, were almost identical, even though the surface morphology was much different. When charge-discharge from 0.02 V to 0.7 V with large-volume change was applied, large cracks were formed on the SEI surface of the C-Si/SiO electrode after shallow cycles, which was similar to that after deep cycles. As a result, the cell properties for shallow cycles corresponded roughly to those for deep cycles. This suggests that the charge-discharge of a C-Si/SiO electrode is strongly related to the surface morphology, meaning that stable cycle properties can be achieved by controlling the morphology of the SEI.