In order to reveal the structural characteristics and vertical distribution patterns of the protozoan community in lakes on the Tibet Plateau in China, a survey was conducted in the center of Basom-tso lake in November 2017, May and September 2018. Sample sites were collected at 7 different dephths of water using the 25# plankton net by a combination of in vivo observation and fixed staining, 195 species(86 species in spring, 93 species in summer and 80 species in autumn)were identified, which belongs to 2 phyla, 11 classes, 24 orders, 43 families, 59 genera. The dominant species were found to be the phylum sarcophagus and the sand shell ciliates. The composition of vertical distribution species and the structure of complex community were shown as:surface layer>middle layer>bottom layer. The species diversity, richness and dominance index were shown as:surface layer>middle layer>bottom layer and the uniformity index was mostly 1. The composition of seasonal distribution species and the structure of complex community were shown as:summer>spring>autumn.The species diversity and richness index were shown as:summer>autumn>spring, the dominance index was shown as:summer>autumn>spring, and the evenness index was shown as:autumn>spring>summer. The dominant species and community structure will decrease with the increase of water depth. The servey had revealed an obvious temporal and spatial heterogeneity with low species diversity and high uniformity.