We derive the rupture process of the 2008 Iwate–Miyagi Nairiku, Japan, earthquake (MJMA 7.2), during which the largest ground acceleration to date, namely, 4022 cm/sec2, was recorded at a hanging-wall station, IWTH25 station of KiK-net, just above the hypocenter. Velocity waveform data (0.1–1 Hz) at 14 strong-motion stations of K-NET and KiK-net, including the borehole records of IWTH25, are inverted using the multi-time-window linear waveform inversion method. We assume a horizontally layered velocity structure model having low-velocity subsurface layers for each station in order to calculate the Green’s functions. The waveform inversion indicates that there are two major slip patches. One patch extends from the hypocenter to the southern shallower part of the fault. A particularly large slip area in this patch is centered approximately 8 km to the south of the hypocenter with a maximum slip of 6.2 m, the area ruptured between 4 and 9 sec after the initial break. The other patch with smaller slip is located in the northern part, which broke after the rupture of the southern slip patch. The initial 0–4 sec rupture occurred beneath IWTH25, contributing to the synthesis of a distinctive upward velocity pulse at this station. Examination of the slip contribution to the synthetic velocity waveforms and comparison of the isochrones with the slip distribution suggest that a peak acceleration greater than 4000 cm/sec2 observed at IWTH25 was generated from the area that is closest to the hypocenter in the southern particularly large slip area.