In this study, the destruction differences among three levels of large flake graphite (−1.0+0.3, −0.3+0.18, and −0.18+0.15mm) ground with gangues were investigated. The results revealed that the destruction degree and destruction rate descended with the decrease of graphite flake granularity, and the most severe destruction occurred for −1.0+0.3mm. The internal microstructure differences of the large flake graphite are precisely the key reason for destruction degree and rate differences. The results of X-ray computed tomography showed that the −1.0+0.3mm large flake graphite with a high porosity of 12.73% contained more pores, cracks, and gangues than the −0.18+0.15mm graphite with a low porosity of 0.097% from 2D and 3D dimensions. These results indicate that the effective protection of the large flake graphite, particularly the super-large flake graphite (−1.0+0.3mm), requires timely separation of them from gangues and individual purification to avoid grinding and flotation with fine flake graphite.