We investigate the annual and local time variations of the wave-4 structures in the plasma density and vertical drift in the low-latitude F region by analyzing the measurements from the first Republic of China satellite (ROCSAT-1) and conducting simulations with the Global Ionosphere and Plasmasphere (GIP) model. The GIP model uses apex magnetic coordinates with International Geomagnetic Reference Field (IGRF) for magnetic field, neutral wind from HWM-07, and thermospheric parameters from the NRLMSISE-00 model. In order to understand how the vertical drifts relate to the longitudinal structure of the topside ionosphere, we apply the equatorial vertical drifts observed from ROCSAT-1 to drive the GIP model. The model well reproduces the longitudinal structure in electron density, and the magnitudes of electron density are comparable with ROCSAT-1 measurement at 600 km. The ROCSAT-1 observations of the vertical drift and plasma density show maximum amplitudes of their wave-4 components in July–September and minimum amplitudes in December–February. An eastward shift of the wave-4 components with increasing local time is observed in both the density and the vertical drift. The GIP model density showed similar annual and local time variations of the wave-4 component. Since the model uses the observed equatorial vertical E × B drift as an input, the results indicate the vertical drifts are essential in the formation and evolution of the longitudinal wave-4 density structure. The amplitude of the eastward propagating diurnal tide (DE3) at 110 km shows similar annual and local time variations as the F region parameters, supporting the link between the DE3 tide, vertical E × B drift, and F region plasma density on a global scale.