The biological pump and deep-ocean ventilation in eastern equatorial Pacific (EEP) Ocean are thought to play a crucial role in cases of global CO2 change. However, the integral role of these two processes in regulating atmospheric CO2 perturbations over major climate transitions are still unknown. Here, we present the magnetofossil record in EEP sediments from Sites 1333 and 1218 across the Eocene-Oligocene Transition (EOT) when the major ice-sheet was first established on Antarctica. We find that the EEP dust fertilization and bottom-water oxygenation were well co-archived by magnetofossil in characteristics of abundance and morphology, respectively. Our observations show a coeval decline of EEP biological productivity and deep-ocean ventilation during the Antarctic glacial expansion, and suggest that the reduced deep-ocean ventilation contributed to the global CO2 decline across the EOT, whereas the superimposed biological pump action provided a negative (stabilizing) feedback in the meantime.