Forming an effective solid electrolyte interphase (SEI) is a significant issue in lithium ion batteries that utilize graphite as a negative electrode material, because the SEI determines the reversibility of the intercalation and de-intercalation of lithium ions into graphite for secondary batteries. In propylene carbonate (PC)-based electrolyte solutions, ceaseless co-intercalation of solvated lithium ions takes place because no effective SEI is formed. It is indisputable that this continuous co-intercalation leads to graphite exfoliation; however, the reason for this is currently not well understood. In this study, we investigate interfacial reactions that contribute to SEI formation on highly oriented pyrolytic graphite (HOPG) in ethylene carbonate (EC) and PC-based electrolyte solutions by in situ atomic force microscopy. The blisters formed on HOPG after the decomposition of solvated lithium ions within the graphite layers do not change over the course of ten electrochemical cycles in an EC-based electrolyte solution. In contrast, when cycling in PC-based electrolytes, the blisters continually change, and the height at the vicinity of the graphite edge plane increases. These morphological changes are attributed to the continuous co-intercalation of solvated lithium ions in PC-based electrolyte solutions.