We derive the 3-D S-wave velocity structures of sediments and upper crust in the region off Ibaraki by applying ambient noise tomography to a dense array of short-period ocean bottom seismometers (OBSs). The cross-spectra were calculated using 27- or 142-day continuous seismic data, and the phase velocities of the fundamental and the first-higher Rayleigh wave modes are obtained in the frequency ranges of 0.1–0.25 Hz and 0.17–0.3 Hz, respectively. Our 1-D S-wave velocity inversion based on the trans-dimensional Markov chain Monte Carlo method revealed multiple sedimentary layers above the acoustic basement and the upper crustal structure. The 1-D structure was then used as a reference model to conduct ambient noise tomography and non-linear inversion of the 3-D S-wave velocity structure by collecting data of the local 1-D S-wave velocity structure. Our 3-D S-wave velocity structure revealed three main points: (1) The acoustic basement is situated at a depth of ~4 km depth; (2) the crustal structure is more complex than the that of the sedimentary layers; and (3) the southern region has a complex crustal structure in which subducting seamounts were identified by previous P-wave velocity tomographies.