Based on a cruise in June, 2010 in Qinzhou Bay, structural characteristics of the phytoplankton community were studied during flood season. Phytoplankton samples from 19 stations were analyzed by RP-HPLC combined with DAD (diode array detector) to determine photosynthetic pigment composition in the study bay. Pigment data were converted into phytoplankton composition by software of CHEMTAX based on least squares method and the steepest descent algorithm. Our results showed that chlorophyll-a (Chl-a), fucoxanthin, chlorophyll-b (Chl-b) and zeaxanthin were the major pigments in Qinzhou Bay. Chl-a concentration ranged from 732 μg/m³ to 9684 μg/m³ (with a mean of 3574μg/m³), and the concentration of fucoxanthin ranged from 51 μg/m³ to 2714 μg/m³ (with a mean of 917 μg/m³). Mean concentrations of Chl-b and zeaxanthin were 161 μg/m³ and 85 μg/m³, respectively. Other pigments generally contributed a minor proportion of the total pigments, with average concentrations of less than 70 μg/m³. Diatoms dominated in the phytoplankton community, contributing to 70.2% (mean value) of the phytoplankton biomass in QinZhou Bay, while the average percentage for cyanobacteria and prymnesiophyta was only 12.6% and 9.4%, respectively. Chlorophyceae was only abundant at the station in Maolingjiang estuary, which accounted for 40% of the phytoplankton biomass. The rest of the other phytoplankton were rare, and constituted <10% of all phytoplankton biomass. Diatom biomass ranged from 0.21μg/L to 8.71 μg/L (Chl-a biomass), and the distribution of diatom biomass was low in the inner bay and high in the outer bay. However, the biomass of cyanobacteria and prymnesiophyta in the inner bay was slightly higher than that in the outer bay. Phytoplankton communities in Qinzhou Bay were clustered into four types from the estuary to the outer bay, and were primarily influenced by floods on the Maolingjiang and Qinjiang rivers. Phytoplankton communities in the estuary were dominated by Chlorophyceae. Diatoms, cyanobacteria and prymnesiophyta were the major groups in the inner bay, while diatoms were dominant in the outer bay. Diatoms also dominated at the offshore stations; however, the proportion of diatoms decreased slightly with increasing distance from the coast. Additionally analysis also was carried out to illuminate the relationship between phytoplankton community structure and environmental factors in the study area. Results indicate that the distribution of major phytoplankton pigments and communities were coupled with environmental parameters in Qinzhou Bay. River flow, salinity and nutrients were the major controlling factors accounting for the spatial distribution and composition of phytoplankton in the bay.