Abstract Seismic and aseismic slip has been reported in the Nankai Trough. In this study we apply ambient noise differential adjoint tomography to obtain a high‐resolution S‐wave velocity (Vs) model in the Nankai Trough. The Vs in the very shallow imbricate thrust zone is higher than that on both the seaward and landward sides. This region may prevent the upward migration of fluids from below, which may lead to an elevated pore fluid pressure beneath the region and facilitate slow earthquake occurrence. There is a large‐scale anomaly with low Vs and high P‐wave velocity (Vp)/Vs in the Kumano basin. This may be caused by the ascent of deep‐sourced fluids from the plate boundary and indicate that an impermeable condition is absent in the seismogenic zone. In subduction zones the permeability property above fluid‐source zones may be important for the strength of the plate interface and thus the types of earthquakes.