Ciliates, as a keystone microorganism in water bodies, link bacteria and phytoplankton and higher trophic levels. Accurate quantitative assessment of ciliates would lead to better predictions of material and energy flux through planktonic food web in lake systems. Ciliates were quarterly collected in 2009 at 32 sampling sites in shallow eutrophic Lake Taihu, fixed by Bouin's solution, and stained by quantitative protargol stain (QPS). In this study, the distribution patterns of ciliate community compositions and functional groups were studied. The relationship between the ciliate community compositions and environmental variables including abiotic and biotic parameters was analyzed by canonical correspondence analysis (CCA). In the 128 samples, a total of 117 species belonging to 3 classes, 15 orders and 78 genera were found. Among the functional groups, 39 species are fallen into the bacterivorous group, represented by orders Scuticociliatida, Hymenostomatida, Peritrichida and Colpodida. Algivorous group had 25 species, mostly belonging to oligotrichids. The mixotrophic, omnivorous and predacious groups had 15, 11 and 10 species, respectively. The rest 17 species belong to the group mainly feeding on heterotrophic flagellates or are in the unclear position. The dominant species were Askenasia acrostomia, Balanion planctonicum, Codonella cratera, Cyclidium glaucoma, Halteria bifurcata, H. grandinella, Rimostrombidium brachykinetum, R. humile, Tintinnopsis cylindrata, Urotricha farcta, Vorticella aquadulcis complex and V. campanula. Ciliate abundance ranged from 1 500 to 139 150 cells/L (mean 27 170 cells/L) and biomass from 16.7 to 8736.0 μg/L (mean 600.6 μg/L). Oligotrichids occupied 45.9% of total ciliate abundance, followed by prostomatids (34.1%), scuticociliatids (11.8%), peritrichids (3.6%) and haptorids (2.6%). The ciliate community compositions had a high heterogeneity and seasonal succession. Ciliate abundance was significantly higher in summer (August) than in other seasons. Their biomass was significantly higher in spring and autumn than in winter and summer. Generally, ciliate abundance had an increase tendency from the south part to north part of Lake Taihu, and from the pelagic area to the littoral. The small-sized species belonging to oligotrichids, scuticociliatids and prostomatids dominated the ciliate communities in the north part of Lake Taihu while the meso- and large-bodied oligotrichids species dominated in the south part. Among the functional groups, the mixotrophic taxa accounted for a substantial proportion of the ciliate assemblages in May and August. The bacterivorous and algivorous taxa dominated in the north and south parts of Lake Taihu, respectively. Unlike the above three groups, the omnivorous, predacious and the others groups only constituted a far smaller percentage of the total ciliate abundance. Results from CCA analysis showed that spatial variations of the ciliate community compositions were determined by difference factors among four seasons. The nitrogen, total dissolved carbon and chlorophyll a content mainly determined the ciliate communities in winter. Copepod, pH, nitrate and ammonium controlled the ciliate communities in spring. The ciliate communities in summer were shaped by copepod, turbidity and dissolved nitrogen, Copepod and total dissolved carbon structured the ciliate communities in autumn. These results illustrated that both the trophic level and predation jointly shaped the ciliate community compositions in Lake Taihu.