The southern Mariana subduction zone features the Earth’s deepest trench, named the Challenger Deep, and tectonic deformation is obvious in the overriding and subducting plates. We conducted a 230 km-long wide-angle reflection/refraction survey across the Challenger Deep. Based on ocean bottom seismometer (OBS) data, we image the velocity structure using forward and inverse modeling. The velocity model shows that the Pacific plate entering the subduction zone has normal crustal thickness (6.5–7.2 km) but lower velocity than mature Pacific oceanic crust. PnP seismic phases with large offsets and strong seismic reflectivity are observed at eight OBS seismic record sections, which constrain the thickness (4.0–6.5 km) and velocity (7.1–7.5 km/s) of the upper mantle low-velocity layer. We suggest that the observed velocity reduction in the crust and upper mantle of the subducting plate is caused by bending-related normal faults, which not only fracture the crust but also provide pathways for water infiltration and serpentinization of the dry mantle. The upper mantle reflector constrained by PnP seismic phases possibly indicates a rheological and fault-slip interface derived from rapid variations in the mechanical strength of peridotite. The inner trench slope (ITS) near the Challenger Deep is characterized by indented topography, where the upper crust is obviously thinned and the lower crust is uplifted; the isovelocity contour of 6.5 km/s is 1.5 km below the seafloor. This may be caused by the difference in the degree of subducting plate rollback on either side of the western boundary of the diffuse deformation zone.