A prominent large-scale traveling ionospheric disturbance (LSTID) was observed in Japan during the major magnetic storm (Dst ~ -358 nT) of 31 March 2001. It was detected as enhancements of the 630-nm airglow and foF2, GPS-TEC variations, and a decrease in F-layer virtual height at 1700--1900 UT (0200--0400 LT). It moved equatorward with a speed of ~600 m/s. The decrease in the F-layer height was also detected by the MU radar at Shigaraki. Thermospheric wind variations were observed by the MU radar through ion drift measurement and by a Fabry-Perot interferometer (FPI) through a Doppler shift of the 630-nm airglow line at Shigaraki. The wind data show a turn of the meridional wind from -94 m/s (equatorward) to +44 m/s (poleward) during the LSTID, indicating that an intense poleward wind in the thermosphere passed over Shigaraki as an atmospheric gravity wave and caused the observed ionospheric features of the LSTID. Intense poleward wind was also detected at mesospheric altitudes (95--100 km) by the MU radar (through meteor echoes) and by the FPI (through the 558-nm airglow) with a delay of ~2 hours from the thermospheric wind, indicating downward phase progression of the wave. Generation of the observed poleward wind in the auroral zone was investigated using magnetic field data and auroral energy input estimated by the assimilative mapping of ionospheric electrodynamics (AMIE) technique. We suggest that simple atmospheric heating and/or the Lorentz force in the auroral zone do not explain the observed poleward wind enhancement.