A theoretical low-latitude ionospheric model was used to study the equatorial anomaly trough (EAT) and analyze factors which contribute to the variations of the EAT location. Model simulations showed significantly diurnal, seasonal and longitudinal variations in the EAT location. The EAT situated to the north of magnetic dip equator at June solstice and shifted to the south at December solstice. It was found that the seasonal variation of the EAT location was mainly caused by neutral winds, not by the seasonal variations in ionic photoionization production rates themselves. Distinct longitudinal variation in the EAT location occurred at the north of dip equator near 285°E and at the south of dip equator near 110°E, which was qualitatively consistent with previous observations. Simulations showed that the longitudinal variation of the EAT location was caused mainly by the longitudinal structure in neutral winds. At most longitudes, the effects of magnetic declination and the displacement between geographical and magnetic equators were negligible. Only at regions near the 330°E longitudes did the magnetic declination play some larger influence on the EAT location, but it was still much smaller than that of neutral winds.