Biogeochemical cycling in the Southern Ocean (SO) plays a key role in the global sea-air CO2 balance and in the ocean anthropogenic carbon inventory (Ito et al., 2010; Khatiwala et al., 2009; Sarmiento et al., 2004). Some previous studies suggest a decreasing trend in the Southern Ocean carbon sink (Le Quere et al., 2007; Lovenduski et al., 2007; Wetzel et al., 2005). We investigate the interannual and decadal variations in sea-air CO2 flux and phytoplankton production in the SO with hindcast simulations by an ocean biogeochemical model. Decreasing trends in sinking POC and primary production are found from 1979 to 2003, concurrent with a decreasing trend in carbon uptake from the atmosphere. Simulations show substantial interannual and decadal variability in productivity. The sea-air CO2 flux is significantly correlated with sinking POC, especially in high productivity regions of the Southern Ocean. Both mixed layer depths and iron concentrations are important to the long-term trends in production and phytoplankton community structure. Sea ice cover also plays an important role at high latitudes. Variability in dust deposition in recent decades has little influence on total SO productivity and carbon uptake, however, there are regional impacts near dust source regions. Accurately representing mixed layer depths and their impacts on phytoplankton light stress are critical for understanding how climate change impacts SO ecosystems and biogeochemistry.