Ionospheric plasma density data from the planar langmuir probe onboard the CHAllenging Minisatellite Payload (CHAMP) are used to investigate the latitudinal profile of the ionosphere. Along with the well-known profiles with features of the equatorial ionization anomaly and equatorial plasma bubbles, a third type is observed as smooth profiles with large scale deep equatorial trough (DET) where the plasma density is extremely low. A global survey focusing on magnetically quiet condition reveals that, the DET profiles are generally a post-sunset phenomenon, and their appearance depends on longitude and season. During equinox seasons in solar active years, the strong pre-reversal enhancement electric field are believed to uplift the ionosphere and produce the DET profiles. While around June solstice, the DET profiles are clustered at 45° W–0° E longitude, where the zonal electric field is weak but the magnetic meridional component of the neutral wind is most significant. The SAMI2 model is then employed to simulate the ionosphere in the magnetic meridional plane with enhanced neutral wind, and successfully reproduces the main features of the DET profile observed. The results indicate that the neutral wind can obviously affect the equatorial ionosphere by transporting plasma in magnetic flux tube through neutral-ion interaction. The neutral wind is previously known to work with inclined magnetic field at mid-latitude, while this study emphasizes its effect around the magnetic equator especially when the electric field forcing (EXB) is weak or absent.