In this study, we conduct an in‐depth analysis of Whole Atmosphere Community Climate Model‐eXtended simulations to examine physical mechanisms of the formation and evolution of an equatorial ionization anomaly (EIA) merging phenomenon during a storm on 4 November 2021. A quantitative analysis reveals that the rapid decay of the EIA crests at their poleward sides at altitudes of ∼200–250 km plays a crucial role in the EIA merging during that day. This rapid decay is due to the fast recombination at low altitudes (∼200–250 km) as the plasma are transported downward by the westward disturbance dynamo electric field and poleward neutral winds during the storm. The results suggested EIA‐merging is not merely northern and southern EIA crests moving together, but it involves a crucial rapid decay of the EIA crests at their poleward sides that descended to low altitudes (rapid recombination, ∼200–250 km), driven by regional electric fields and neutral winds. This study plays a crucial role in our understanding of the evolution and formation of the merged EIA on 4 November 2021 during the storm.