Understanding the structure and formation dynamics of the solid electrolyte interphase (SEI) on the electrode/electrolyte interface is of great importance for lithium ion batteries, as the properties of the SEI remarkably affect the performances of lithium ion batteries such as power capabilities, cycling life, and safety issues. Herein, we report an in situ electrochemical scanning tunnelling microscopy (ECSTM) study of the surface morphology changes of a highly oriented pyrolytic graphite (HOPG) anode during initial lithium uptake in 1 M LiPF₆ dissolved in the solvents of ethylene carbonate plus dimethyl carbonate. The exfoliation of the graphite originating from the step edge occurs when the potential is more negative than 1.5 V vs. Li⁺/Li. Within the range from 0.8 to 0.7 V vs. Li⁺/Li, the growth of clusters on the step edge, the decoration of the terrace with small island-like clusters, and the exfoliation of graphite layers take place on the surface simultaneously. The surface morphology change in the initial lithium uptake process can be recovered when the potential is switched back to 2.0 V. Control experiments indicate that the surface morphology change can be attributed to the electrochemical reduction of solvent molecules. The findings may lead to a better understanding of SEI formation on graphite anodes, optimized electrolyte systems for it, as well as the use of in situ ECSTM for interface studies in lithium ion batteries.