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Abstract The extension of the neutral sodium (Na) layer into the thermosphere (up to 170 km) has recently been observed at low and high latitudes using a Na lidar. However, the geophysical mechanisms and implications of its formation are currently unknown. In this study, we conduct an advanced two‐dimensional numerical simulation of the Na and Na⁺variations in theEandFregions at low latitudes. The numerical simulations are used to investigate the contributions of the electromagnetic force, neutral wind, diffusion, and gravity. The simulations lead to three major findings. First, Na⁺in the subtropical region of the geomagnetic equator acts as the major reservoir of the neutral sodium, and its distribution during nighttime is mostly below 200 km due to the combined effect of the vertical component of thedrift and Coulomb‐induced drift. Second, we find that the fountain effect has little influence on the behavior of Na in the nighttime. Third, the probable explanation for the frequent generation of the thermospheric sodium layer during spring equinox at Cerro Pachón, Chile is attributed to the large vertical neutral transport generated by large vertical wind perturbations of unknown origin, with a magnitude exceeding 10 m/s that is closely associated with the semidiurnal tide.