A three-dimensional coupled model of the global ionosphere and thermosphere has been used to examine the importance of ion drag parallel to the geomagnetic field, on the equatorial wind and temperature structure. Simulations performed at equinox, moderate solar activity (F10.7 = 150), and geomagnetically quiet condition (Ap = 7) show that the model reproduces the general observed structures of the global ionosphere and thermosphere. Comparison between the model results and satellite observations confirms that ion drag plays a significant role in the zonal momentum balance and superrotation of the Earth's upper atmosphere at equatorial latitudes. The results also suggested that ion drag parallel to the field lines, in the vicinity of a pronounced Equatorial Ionization Anomaly, has a significant impact on the latitudinal structure of the equatorial neutral wind and temperature structure. Note that the impact of parallel ion drag on the wind and temperature structure has not been evaluated previously. The model simulations show that the ion motion parallel to the field lines acts as a source of momentum to the neutral atmosphere. It is well established that after being transported upward by electric fields at the magnetic equator, plasma falls along the inclined field lines either side. The simulations indicate that collisions between the falling plasma and neutrals impart a small momentum source forcing poleward winds away from the magnetic equator. The neutral wind in turn transports momentum and energy and produces adiabatic changes that alter the meridional temperature structure. The results show that the impact of parallel ion drag must be considered in any comprehensive analysis of dynamics and energy coupling of the equatorial ionosphere and thermosphere and is important when interpreting observations of equatorial wind and temperature features, such as ETWA or MTM.