The formation and evolution of the solid electrolyte interphase (SEI) film on the surface of natural graphite spheres in the electrolyte of 1 M LiPF6 in ethylene carbonate (EC) and dimethyl carbonate (DMC) (volume ratio 1: 1) were investigated with use of focused ion beam (FIB) technology. Secondary electron FIB images clearly show the surface and cross-section morphology of the SEI film. The composition variation along the surface and cross section of the SEI film was also explored by the elemental line scan analysis (ELSA). The initial SEI film with an apparent thickness range of similar to 450 to similar to 980 nm is rough in morphology and nonuniform in composition, and contains small splits. After certain electrochemical cycles, the thickened SEI film displays microscale holes and obvious cracks on the surface, and the content of organic compounds increases. In addition, the concept of "internal SEI film" is first proposed based on the characterization of the cross section of the natural graphite spheres with the aid of FIB. Finally, the capacity fading mechanisms of the natural graphite spheres corresponding to different electrochemical stages are discussed.