Satellite remote sensing and numerical models are widely used to estimate large-scale variations in ocean carbon export, but the relationship between export efficiency (e-ratio) of sinking organic carbon out of the surface ocean and its drivers remains poorly understood, especially in the Southern Ocean. Here, we assess the effects of temperature and primary productivity on e-ratio by combining particulate organic carbon export flux from in situ measurements during 1997-2013, environmental parameters from satellite products, and outputs from ocean biogeochemical models in the Southern Ocean. Results show that "High Productivity Low E-ratio" (HPLE) is a common phenomenon in the Subantarctic Zone and the Polar Frontal Zone, but not the Antarctic Zone. The e-ratio shows little dependence on temperature below 6 °C. Our results support the hypothesis that the HPLE phenomenon is due to the large contribution of non-sinking organic carbon. Both temperature and ballast minerals play less important roles in controlling e-ratio than ecosystem structure at low temperatures. These findings suggest that non-sinking organic carbon, ecosystem structure, and region-specific parameterizations of e-ratio are key factors to quantify the carbon export in the Southern Ocean.