We apply Frequency-domain Waveform Tomography to form quantitative, high-resolution P-wave velocity images of a megasplay fault system within the central Nankai subduction zone offshore of southwest Japan, using controlled source Ocean Bottom Seismometer (OBS) data originally acquired in 2004. The Waveform Tomography method exploits recorded seismic waveforms beyond their first arrivals, and thus achieves a much higher resolution (of the order of a wavelength) than that of conventional Traveltime Tomography methods. Frequency-domain Waveform Tomography facilitates a multi-scale approach to stabilize the inversion, in which initial Traveltime Tomography results are sequentially improved on by first fitting low frequency components of the seismic records (starting at 2.25Hz); higher frequency components (up to 8.5Hz) are then introduced progressively. Our final Waveform Tomography image allows velocity anomalies as small as 700m (horizontally) and 350m (vertically) to be discerned and interpreted, as confirmed by checkerboard modeling tests. The improved explanatory power of the final images is verified by observing that synthetic waveforms calculated from the final results yield much better fit to the observed waveforms than those estimated from the original Traveltime Tomography image. Apparent lithological boundaries from Waveform Tomography agree well with corresponding reflections on seismic migration images, providing further confidence in the validity of the results. The megasplay fault is evident on the final Waveform Tomography image as a sharp velocity discontinuity, delineating the upper surface of a velocity reduction of nearly 1km/s with respect to the regional 1D velocity trend. The megasplay fault can be traced continuously throughout the entire image, from a nearly horizontal section at the landward extent, moving seaward through to a steeper angle penetrating the old accretionary prisms, with several additional splays appearing to branch in the shallow subsurface. The location of the low-velocity zones imaged by our waveform tomography method coincides with two-previously-identified low velocity zones. The image reveals a low velocity zone that is continuous from deeper to shallower portions of the subsurface, suggesting that pore-fluids may be transported from the inner wedge, to the transition zone, and to the surface, through fluid conduits associated with the megasplay fault system.