The study on population dynamics of phytoplankton was still an important basic work for ecological investigations in large rivers. Through continuous sampling at the downstream of Xijiang River in 2009, the annual variation pattern of phytoplankton community structure and its correlation with environmental factors were demonstrated in this study. During the investigation, the 245 taxonomic species (including variant and derivative) in 7 groups were identified. The results showed that the diatom (Bacillariophyaceae) and chlorophytes were most abundant and they were 42.44% and 34.69% to total numbers respectively, and the Euglenophyta and Cyanobacteria were subsidiary to them. The above structure pattern was the similar to those of other large rivers in the world. 15 main species (dominant and frequent species) were listed in table 1, but only 3 species showed both high biomass contribution and high occurrence. For all the species, Aulacoseira granulata var. granulata was the predominant one because it showed continuous dominance except for its biggest occurrence. The annual variation pattern of total species abundance was high in warm seasons and low in cold seasons, which was also consistent with the diatom and green algae group. One reason is that many species favorite the high water temperature and the other is that the high discharge of warm seasons could also promote the inoculations from out-of-channel sources of true planktonic green algae and the complement of tychoplanktonic diatom species. This result has been confirmed by the annual pattern of true planktonic species richness, since the true planktonic diatom showed almost steady during the whole year, and the PCA analysis confirmed the two key factors. The annual phytoplankton biomass showed apparent bimodal pattern, and the two peaks appeared after the flood period. In addition, the biomass values showed almost no fluctuations besides the two peaks, which was because that the positive role of rising water temperature was covered by the negative role from the dilution impact of high discharge. According to the previous studies, self-sustaining populations of riverine algae were primarily based on meroplanktonic diatom species, whereas true planktonic populations, mostly chlorophytes depended on periodic inoculations from outer sources. Therefore, diatom would apparently precede chlorophytes when water discharge increased. In conclusion, the diatom and green algae were the most important groups of phytoplankton community in Xijiang River, and their annual variation pattern could strictly affect the total phytoplankton community. The phytoplankton species abundance was mainly determined by the true planktonic green algae and tychoplanktonic diatoms, and both water temperature and water discharge were the main reasons for their increments, and Si concentration was only beneficial for diatoms. The phytoplankton biomass was mainly determined by several dominant species (especially the true planktonic diatom species), and water temperature and discharge played important roles for the phytoplankton biomass during the seasons.