The growth, cellular total lipids, bioaccumulation amount, and bioaccumulation factors (BAFs) of 2,4,4'-tribromodiphenyl ether (BDE28), 2,2',4,4'-tetrabromodiphenyl ether (BDE47), and 2,2',4,4',5-pentabromodiphenyl ether (BDE99) in a semi-continuous culture of Prorocentrum donghaiense were studied in relation to nitrate (0, 128, and 512 μupmol/L) and phosphate (0, 8, and 32 μupmol/L) concentrations. The BDE28, BDE47, and BDE99 content per cell under 0 μupmol N/L were 3.77×10-6, 3.95×10-6, and 4.32×10-6 ng/cell, respectively, which were significantly higher than those under 128 and 512 μupmol N/L. A nearly 5-fold increase in polybrominated diphenyl ether (PBDE) content per algal cell was found between 0 and 8 μupmol P/L and between 8 and 32 μupmol P/L. With increasing N and P concentrations, the PBDE content per volume of algal culture and the accumulation percentage of available PBDEs declined slightly. The BAFs for the PBDEs based on lipids showed that the logBAFlip under 0 μupmol N/L was higher than those under 128 and 512 μupmol N/L. The logBAFlip under 0 μupmol P/L was higher than that under 8 μupmol P/L but lower than that under 32 μupmol P/L. Correlation analysis indicated a significant negative correlation between nutrient concentration and cellular total lipids, as well as the PBDE content per cell. The results indicate that different N and P concentrations change the total lipids content of P. donghaiense, thereby resulting in varying PBDE accumulation.