In order to explore the community structure of planktonic ciliates in the Tibetan plateau river of China and their relationship with the environmental factors, investigation was carried out from August 2015 to November 2016 in the upper and middle reaches of the Lhasa River. A total of 64 samples were collected from eight representative areas using 25# standard plankton net. Species identification using live observation and fixed-staining method. As a result, 91 species of ciliates were identified in this study:49 species in summer, the order of species number in eight areas is as follows:S2 < S4 < S8 < S5 < S1 < S3=S7 < S6; 64 species in autumn, the order is:S4 < S3=S1=S2=S5 < S8 < S6=S7. The abundance of ciliates of each area was ranged from 1.2×10⁴ ind/L to 5.6×10⁵ ind/L in summer, and from 1.2×10⁴ ind/L to 2.6×10⁵ ind/L in autumn. There were 12 dominant species in summer and autumn, respectively, but the composition and distribution were different, which revealed the spatial and temporal variation in ciliates in this basin. The community structure analysis indicated that the ciliate community has a simple structure, low diversity, and uniform distribution. The structural analysis of the nutritional function of ciliates showed that the abundance of B and S groups in summer was lower than that in autumn. Correlation analysis suggested that total phosphorus and total nitrogen were main environmental factors which influenced the diversity of summer ciliates; additionally, turbidity, NH₄-N, and NO₃-N were the main environmental factors influencing autumn ciliates.