The presence of Late Quaternary faults in the Pearl River Delta region is an important factor that may affect the development of the Greater Bay Area. Loose Quaternary sediments within active fault zones are the main markers and information carriers of fault activity, comprehensive observations of loose sediments from the point view of three-dimension are difficult. In this study, borehole cores from the main fault zones in Xilingang, Guangzhou were X-ray CT scanned using whole-core scanning devices, images were processed and visualized by using the volume rendering technique to investigate the 3D structures of the cores focusing on the deformation of Quaternary unconsolidated sediments. The study demonstrates that the CT scan of borehole cores enables us to virtually observe cores with reality from different perspectives by free rotations, which is impossible to reach physically for unconsolidated cores, and further reveals a large number of phenomena that cannot be observed from conventional core photographs, including the internal heterogeneous structures, the distribution of materials, and the extending pattern and compositions of fractures. Combined with the dating results of sediments, the time of fault activity can be estimated. Therefore, whole-core CT scanning can be a preferred new method for studying unconsolidated borehole cores and is recommended for geological exploration and active fault investigations in areas covered by soft sediments.