The Arctic and Antarctic marginal seas play their important roles in global ocean carbon flux and living resources, yet their ecosystems experience dramatic seasonal shifts in habitat conditions and food availability. Zooplankton exhibit substantial seasonal variations in distribution, behavioral traits and carbon export, with stark contrasts between productive spring–summer and unproductive autumn–winter periods. A Joint Transdisciplinary Ecosystem Study (JTRES) was carried out in the Ross Sea during austral fall (March–April) 2025 to examine ecosystem structure and biogeochemical processes against those of spring and summer. Our results document the seasonal downward migration of mesozooplankton to deep waters over the continental shelf and slope, alongside dense aggregations of Antarctic krill along the slope and off-slope zones. Via vertical migration, mesozooplankton transport large quantities of biomass accumulated in the surface mixed layer over summer to deep waters, where the biomass is consumed and remineralized throughout winter. Antarctic krill actively aggregate and forage in both surface and deep layers. We compared the total biomass of mesozooplankton and krill against the standing stock of accumulated primary production. The vertical migration and trophic consumption of mesozooplankton and krill constitute a critical overwintering strategy for these populations, while serving as major pathways for vertical upward and downward carbon fluxes.