This paper reports on the study on the protozoan community structure of the immersed sediment in the Three-Gorges Area of the Changjiang River. Protozoa observed included 7 phytoflagellates, 12 zooflagellates, 49 amoebae and 16 ciliates. Sarcodina dominated in sediment, ciliates in water. Analysis of species and horizontal density distribution of protozoan in sediment in 28 sampling points reflected the pollution degree of water quality at every site. It was shown that heavy metal contamination in sediment has some effects on the distribution of protozoan species in the Changjian River.