The settling of particulate carbon in seawater is a key component of the ocean carbon cycle. We deployed a set of sediment trap in the polynya of Prydz Bay from December 2010 to December 2011 to investigate the seasonal variations in particle fluxes. There was a clear seasonal variation in the particle fluxes, with maximum and minimum fluxes recorded during the summer and winter, respectively. The average total flux over the sampling period was 193.58 mg m−2 d−1, and the average fluxes of organic carbon (Corg), inorganic carbon (Cinorg), and biogenic silica (Sibio) were 721.78, 28.67, and 2382.80 μmol m−2 d−1, respectively. Sibio was the main contributor to the total mass flux, and strongly correlated with Corg. The high Sibio/Corg molar ratios (>1) suggest that Corg was transported to deep sea in association with Sibio. By comparing remote sensing data of sea ice and chlorophyll in the upper water column, we found that the dynamics of carbon fluxes were closely related to changes in sea ice. Algae in sea ice may have a key role in biological pump processes in early summer. Apart from the ice algae bloom period, variations in carbon fluxes generally corresponded with phytoplankton blooms in the upper water. The ballast effect controlled the particle settling velocity and the efficiency of the biological pump. Sea ice rafts initiated the first particle export event and enhanced the particle settling efficiency during melting period. As diatoms might become less dominant in the ice-free area, sea ice loss may cause the efficiency of the biological pump efficiency to decrease over the long term.