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.