Tropical cyclones are increasingly affecting the estuarine communities. Impacts of category-5 tropical cyclone Amphan (landfall on 20 May 2020 near Ganges estuary mouth) on the copepod community of Muriganga section of Ganges estuary was studied by sampling the copepod assemblages before (February to December 2019), shortly after (31 May to 12 June 2020) and post (September to November 2020) cyclone. Hypothesis was shortly after Amphan a relatively homogenous community consists of a few estuarine specialist copepods would succeed but within months that community would be replaced by a heterogenous one but those estuarine specialists would continue their dominance. Shortly after Amphan, species richness declined but the recovery process completed within months led by herbivorous Paracalanus parvus, omnivorous Bestiolina similis, Acartia spinicauda, Acartiella tortaniformis, and carnivorous Oithona brevicornis. Spatial homogeneity of the community that prevailed in Muriganga in pre-Amphan and shorty after Amphan was lost in post-Amphan. Community composition changed from pre- to shortly after to post-Amphan. Unilateral dominance of B. similis observed in pre-Amphan was challenged by P. parvus, A. spinicauda, A. tortaniformis and O. brevicornis shortly after Amphan and in post-Amphan. Acartia spinicauda proliferated shortly after Amphan and co-dominated the estuary along with A. tortaniformis but the latter replaced the former in post-Amphan. Copepods did rebuild their community within a few months from Amphan but experienced rearrangements of species composition, abundance, dominance hierarchy and feeding guilds, which may strain benthic-pelagic linkages of Ganges estuary so shall be monitored regularly by coastal institutions following uniform methods and best practises.