Abstract: In this study, we explored the seasonal change in the structure of the phytoplankton community in the head region of the Three Gorges Reservoir (TGR). Field sampling was carried out in August (summer) and November (autumn) of 2012 and in January (winter) and April (spring) of 2013. Eight phyla and 151 genera and species were identified, including 71 species of Chlorophyta, 47 species of Bacillariophyta, 20 species of Cyanophyta, 4 species of Pyrrophyta and Cryptophyta, 2 species of Chrysophyta and Euglenophyta, and 1 species of Xanthophyta. Bacillariophyta and Chlorophyta were the most abundant phyla. There were remarkable seasonal variations in the composition of the dominant phytoplankton species. The dominant species in summer were Cyclotella sp., Pandorina morum, Chlamydomonas sp., Chlamydomonas conica, and Eudorina elegans. The dominant species in autumn were Cyclotella sp., Melosira sp., and Chlorella vulgaris. In winter, the dominant species were Cyclotella sp., Aphanizomenon sp., Phormidium sp., Merismopedia tenuissima, Pseudanabaenaceae sp., and Lyngbya sp. In spring, the dominant species were Chlamydomonas sp., Cyclotella sp. and Chroomonas acuta. The abundance of phytoplankton peaked in summer and reached the lowest in autumn. The annual density and biomass were 3.950106 ind./L and 4.078 mg/L respectively. The abundance of phytoplankton in the bay and the tributary was higher than that in the mainstream. The water body in the head of region TGR was lonsidered to be -mesosaprobic according to the diversity index of the phytoplankton community. Our study provided insights into the spatial and temporal dynamics of the phytoplankton community structure and will helpus develop strategies to improve the water quality in the TGR.