Multipoint ionosonde observation was conducted in Southeast Asia to study ionosphere‐thermosphere coupling. For this observation three ionosondes were installed along the magnetic meridian at 100°E (Southeast Asia Low‐latitude Ionospheric Network: SEALION); two of them were at magnetic conjugate points and the third was near the magnetic equator. The F layer virtual height, h′F, was scaled from nighttime ionograms obtained from September 2004 to August 2005, close to the solar minimum. The height variations at the three locations were used to derive thermospheric winds in the magnetic meridional plane for transequatorial and convergent/divergent components (with respect to the magnetic equator). During northern winter months, a prominent 6‐hr periodic variation of a transequatorial component was found. During northern summer months, a diurnal or semidiurnal variation was dominant. Convergent winds toward the magnetic equator were associated with the occurrence of the midnight temperature maximum at the latitudes between the two conjugate stations as observed by satellite instruments during the solstices. However, no clear evidence was found of abatement of the wind due to the pressure bulge associated with the midnight temperature maximum.