Mesozooplankton play a crucial role as primary or secondary consumers in Arctic ecosystems and are sensitive indicators of environmental changes. This research is the first comprehensive Arctic zooplankton study covering the area ranging from the southern Chukchi Sea (SCS) and the northern Chukchi Sea (NCS) to the East Siberian Sea (ESS). Mesozooplankton samples were collected at 151 stations in the western Arctic Ocean each August from 2016 to 2020. The mesozooplankton abundance of the study area ranged from 9 to 6,172 ind. m−3, and the predominant group was copepods at 7–3,866 ind. m−3, of which Pseudocalanus spp. and Calanus glacialis were the most abundant copepods. In the SCS, small copepods and meroplankton, such as Pseudocalanus spp., Cirripedia larvae, Echinodermata larvae, and Centropages abdominalis were the predominant taxa. Especially in 2019, C. abdominalis dominated over meroplankton when water temperatures were high (maximum 12.5°C; sea surface temperature, SST). In the NCS and ESS, C. glacialis, Pseudocalanus spp., Metridia longa, Oithona similis, Parasagitta elegans, and Calanus hyperboreus were abundant. The distributions and structures of mesozooplankton communities indicated variability over large spatial scales in the western Arctic waters because of variations in multiple factors, such as water temperature, salinity, and sea ice; however, geographical effects cannot be ignored even during alterations in the physical properties. Our results suggest that these variable patterns of mesozooplankton communities fluctuate horizontally from south to north as warming progresses on a regional bathymetric basis, and can be used to infer the fate of mesozooplankton communities in the study area.