Abstract: An anomalous feature of low latitude ionosphere is the Equtorial Anomaly, and measurements show that the minimum peak density located between two crests of the Equtorial Anomaly, the equatorial anomaly trough (EAT), is not always located at near the magnetic equator. A two-dimensional theoretical low-latitude ionospheric model is used to simulate the evolution of the EAT and investigate effects of some physical factors on the location of the EAT. Each of them is adjusted respectively to study their influences on the EAT. Simulation results show that there are extinct diurnal, seasonal and longitudinal variations of the location of EAT. The EAT situates at the north of the magnetic dip equator at June solstice and shifts to the south at December solstice. It is found that the seasonal variation of the position of EAT is mainly caused by the neutral winds, not by seasonal changes in photoionization productions directly due to the variation of the geomagnetic solar zenith angle. Longitudinally speaking, the EAT lies north near 285°E and south near 100°E, which is basically consistent with previous observations. And its longitudinal variation is pricipally caused not by the magnetic declination and displacement between the geographical and magnetic equators, but by the longitudinal changes of horizontal neutral wind, which does not support the previous opinion. 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. In addition, the displacement between the dip equator and equatorial electrojet is not taken into account because the ionospheric model is under the dipole field assumption.