The organic carbon particle export to the interior layers in the Southern Ocean in the New Zealand–Tasmania Sector was approximately 170 mmolC m−2 yr−1. The export of particulate inorganic carbon in CaCO3 was 110 mmolC m−2 yr−1 and was contributed mostly by pteropods shells in the Antarctic Zones. The Si flux from biogenic opal at the sub-Antarctic Zone was 67 mmolSi m−2 yr−1 and rapidly increased to the south up to nearly 1 molSi m−2 yr−1 in the Antarctic Zone. The Antarctic Polar Front clearly demarcated the area where the biological pump was driven by CaCO3 to the north and biogenic SiO2 particle export to the south. Summer stratification caused by the sub-zero winter water layer in the Seasonal Ice Zone (SIZ) curtails the zooplankton community and hinders the replenishment of Fe. This hypothesis explains the large organic carbon export with large f- and export ratios at the SIZ and extremely large opal production at the Antarctic Circumpolar Zone. Estimated regeneration rate of CO2 from the export production and settling particulate fluxes of organic carbon in the water column between 100 m to 1 km was about 13 mmolC m−2 d−1 in the Antarctic Zone and Polar Frontal Zone.