Structural characteristics of phytoplankton community during normal season in 2010 in Qinzhou bay were studied. Phytoplankton samples were analyzed by RP-HPLC combined with DAD (diode array detector) to determine photosynthetic pigments composition in the study bay. Pigments data were converted into phytoplankton composition by software CHEMTAX based on least square method and steepest descent algorithm. Our results showed that salinity in the bay ranged from 14.2 to 31.0, and nitrate as well as phosphate concentrations decreased as salinity increasing from the top of bay to outer bay, which showed typical estuarial characteristics. Chlorophyll-a (Chl-a), fucoxanthin, chlorophyll-b (Chl-b), prasinoxanthin and zeaxanthin were the major pigments in the Qinzhou bay. Chl-a concentration ranged from 2693 μg/m³ to 4338 μg/m³ (with a mean of 3529 μg/m³), and the concentration of fucoxanthin ranged from 390 μg/m³ to 1081 μg/m³ (with a mean of 629 μg/m³). Mean concentrations of Chl-b, prasinoxanthin and zeaxanthin were 304 μg/m³, 66μg/m³ and 65 μg/m³, respectively. Other pigments generally contributed minor proportion of the total pigments, with average concentrations of less than 50 μg/m³. Diatoms dominated in the phytoplankton community, contributing to 76% (mean value) of the phytoplankton biomass during normal season in the Qinzhou Bay, while the average percentage for prasinophyceae and cyanobacteria was only 12.2% and 5.5%, respectively. The rest of other phytoplankton was rare, which only took < 10% of all phytoplankton biomass. Diatoms biomass ranged from 1.49×10³μg/m³ to 3.98×10³μg/m³ (Chl-a biomass), and the distribution of diatom biomass showed a pattern of low in the inner bay while high in the outer bay. However, the biomass of prasinophyceae showed a pattern of decreasing from the inner bay to the outer bay. Phytoplankton communities in the Qinzhou bay were clustered into three types from the estuary to the outer bay,which were primarily influenced by flood of the Maolingjiang River and Qinjiang River. Diatoms together with cyanobacteria and prasinophyceae were the major groups in the estuary of Maolingjiang River and the Qinjiang River, while diatoms were dominated between the inner bay and the outer bay. Diatoms also dominated in the offshore stations of the outer bay, and the proportion of diatoms increased a little and diatoms became a single dominated group. The distribution of major phytoplankton pigments and community were coupled with the environmental parameters in the Qinzhou Bay. River flow, salinity and nutrients were the major controlling factors accounting for the spatial distribution and composition of phytoplankton in the bay during the normal season.