Abstract. Nocturnal ionospheric height variations were analyzed along the meridian of 100 • E by using ionosonde data. Two ionosondes were installed near the magnetic conjugate points at low latitudes, and the third station was situated near the magnetic equator. Ionospheric virtual heights were scaled every 15 min and vertical E×B drift velocities were inferred from the equatorial station. By incorporating the inferred equatorial vertical drift velocity, ionospheric bottom heights with the absence of wind were modeled for the two low-latitude conjugate stations, and the deviation in heights from the model outputs was used to infer the transequatorial meridional thermospheric winds. The results obtained for the September and March equinoxes of years 2004 and 2005, respectively, were compared, and a significant difference in the meridional wind was found. An oscillation with a period of approximately 7 h of the meridional wind existed in both the equinoxes, but its amplitude was larger in September as compared to that in March. When the equatorial height reached the maximum level due to the evening enhancement of the zonal electric field, the transequatorial meridional wind velocity reached approximately 10 and 40 m/s for the March and September equinoxes, respectively. This asymmetry of the ionosphere-thermosphere system was found to be associated with the previously reported equinoctial asymmetry of equatorial ionospheric irregularities; the probability for equatorial irregularities to occur is higher in March as compared to that in September at the Indian to Western Pacific Correspondence to: T. Maruyama (tmaru@nict.go.jp) longitudes. Numerical simulations of plasma bubble developments were conducted by incorporating the transequatorial neutral wind effect, and the results showed that the growth time (e-folding time) of the bubble was halved when the wind velocity changed from 10 to 40 m/s.