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During the storm on 3 and 4 November 2021, the Global‐scale Observations of the Limb and Disk (GOLD) mission observed well separated equatorial ionization anomaly (EIA) crests post sunset on 3 November, but merged EIA on 4 November. We used the Whole Atmosphere Community Climate Model‐eXtended to simulate the EIA structures during the two nights. The simulations show two separated post sunset EIA crests on 3 November but merged post sunset EIA crests on 4 November, which are qualitatively consistent with the GOLD observations. Numerical simulations and Ionospheric Connection Explorer neutral wind observations illustrate that the formation of merged EIA crests was due to several hours of downward E × ${\times} $ B drifts before and after sunset. Further diagnostic analysis revealed that it was mainly driven by westward electric fields caused by the disturbance dynamo electric field during the recovery phase of the storm. Plain Language Summary: The Ionospheric equatorial ionization anomaly (EIA) occurs almost every day and has been studied extensively. A large number of studies have shown that EIA has usually two separated electron density crests around ± $\pm $15° off the magnetic equator in the ionosphere. A structure of merged EIA with just one density crest located near the magnetic equator was observed by a satellite on 4 November 2021. We successfully simulate the merged EIA structure using a first‐principles model. Analysis of the model results reveals that thermospheric neutral winds were disturbed by a geomagnetic storm on 3 and 4 November 2021; the disturbance dynamo electric field due to the disturbed winds changed the usual drift pattern of the plasma, which eventually drive the ionospheric plasma to move toward the magnetic equator causing the merged EIA structure. Key Points: Merged equatorial ionization anomaly (EIA) structure was observed by Global‐scale Observations of the Limb and Disk during the storm of 3 and 4 November 2021This EIA structure was successfully reproduced by Whole Atmosphere Community Climate Model‐eXtended simulationsModel diagnostic analysis reveals that the merged EIA was mainly driven by disturbance dynamo electric fields during the storm [ABSTRACT FROM AUTHOR]