The formation of a longitudinally periodic plasma density structure in the low-latitude F region by the effect of vertical E×B drift was investigated by analyzing the ROCSAT-1 satellite data and conducting SAMI2 model simulations. The daytime equatorial ionosphere observed during the equinox in 1999–2002 from ROCSAT-1 showed the formation of wave number-4 structures in the plasma density and vertical plasma drift. The coincidence of the longitudes of the peak density with the longitudes of the peak upward drift velocity during the daytime supported the association of the longitudinal density structure with the vertical E×B drift. The reproduction capability of the observed wave-4 structure by the effect of vertical E×B drift was tested by conducting SAMI2 model simulations during the equinox under solar maximum condition. When the ROCSAT-1 vertical drift data were used, the SAMI2 model could reproduce the observed wave-4 density structure in the low-latitude F region. On the other hand, the SAMI2 model could not reproduce the observed wave-4 structure using the Scherliess and Fejer vertical E×B drift model. The observation and model simulation results demonstrated that the formation of the longitudinally periodic plasma density structure can be explained by the longitudinal variation of the daytime vertical E×B drift.