Imaging via pre-stack depth migration (PSDM) of reflection towed-streamer multichannel seismic (MCS) data at the scale of the whole crust is inherently difficult. This is because the depth penetration of the seismic wavefield is controlled, firstly, by the acquisition design, such as streamer length and air-gun source configuration, and secondly by the complexity of the crustal structure. Indeed, the limited length of the streamer makes the estimation of velocities from deep targets challenging due to the velocity–depth ambiguity. This problem is even more pronounced when processing 2-D seismic data due to the lack of multi-azimuthal coverage. Therefore, in order to broaden our knowledge about the deep crust using seismic methods, we present the development of specific imaging workflows that integrate different seismic data. Here we propose the combination of velocity model building using (i) first-arrival tomography (FAT) and full-waveform inversion (FWI) of wide-angle, long-offset data collected by stationary ocean-bottom seismometers (OBSs) and (ii) PSDM of short-spread towed-streamer MCS data for reflectivity imaging, with the former velocity model as a background model. We present an application of such a workflow to seismic data collected by the Japan Agency for Marine-Earth Science and Technology (JAMSTEC) and the Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER) in the eastern Nankai Trough (Tokai area) during the 2000–2001 Seize France Japan (SFJ) experiment. We show that the FWI model, although derived from OBS data, provides an acceptable background velocity field for the PSDM of the MCS data. From the initial PSDM, we refine the FWI background velocity model by minimizing the residual move-outs (RMOs) picked in the pre-stack-migrated volume through slope tomography (ST), from which we generate a better-focused migrated image. Such integration of different seismic datasets and leading-edge imaging techniques led to greatly improved imaging at different scales. That is, large to intermediate crustal units identified in the high-resolution FWI velocity model extensively complement the short-wavelength reflectivity inferred from the MCS data to better constrain the structural factors controlling the geodynamics of the Nankai Trough.