The Arctic Ocean is characterized as the greatly variable oceanic environment both seasonality and regionally. Such environmental variability would affect regional differences in the respective copepod community structures, though it has not been reported so far. In this study, we analyzed time-series zooplankton samples with focus on large copepods collected by sediment traps moored in three different regions of the Arctic Ocean at approximately 72–260 m water depth, and seasonality of copepod community structures were compared. Remarkable seasonality in the copepod community structure around Molloy deep in the eastern Fram Strait were due to the influence of endemic species transported by the West Spitsbergen Current. In contrast, in the southern Canada Basin (Northwind Abyssal Plain, Hanna Canyon and Barrow Canyon), the community structure of predominant large copepods showed less seasonality due to low primary production. In the MacKenzie Trough, the number of copepod swimmers were greater than those in all other regions investigated, which cooccur with much higher primary production in that area. These spatial differences in seasonality of copepod swimmer community structure were thought to be caused by various factors, not only sea ice seasonality but also differences in current patterns, endemic species and the magnitude of primary production.