The Southern Ocean plays an important role in modulating Pleistocene atmospheric CO2 concentrations, but the underlying mechanisms are not yet fully understood. Here, we report the laser grain-size distribution and Mn geochemical data of a 523 kyr-long sediment record (core ANT30/P1-02 off Prydz Bay; East Antarctica) to trace past physical changes in the deep Southern Ocean. The core sediments are predominantly composed of clay and silt-sized material. Three grain size end-members (EM) as well as three sensitive grain size classes (SC) were discerned, interpreted as Ice Rafted Debris (EM1 and SC1), and coarse (EM2 and SC2) and fine (EM3, SC3) materials deposited from bottom nepheloid layers, respectively. Ratios of EM2/(EM2+EM3) and SC2/SC3 reveal changes in the local bottom current strength, which is related to the deep ocean diapycnal mixing rate, showing higher values during interglacial periods and lower values during glacial periods. MnO was enriched at each glacial termination, probably caused by abrupt elevations in Antarctic bottom water (AABW) formation rate. Lower AABW formation rate and reduced deep diapycnal mixing during glacial periods enhanced deep Southern Ocean stratification, contributing to glacial atmospheric CO2 drawdown. The elevated AABW formation and enhanced deep diapycnal mixing during glacial terminations alleviated such deep stratification, promoting deeply sequestered CO2 to outgas.