In this study, water samples of lakes with different salinities (fresh, saline and salt) lakes in the QTP were collected to analyze the structural characteristics and driving mechanisms of algae communities, and the Null model was used to quantify the process of algal community assembly processes. The results indicated: The abundance indices of algae in fresh lakes were the highest (average Shannon and Chao1 were 3.60 and 390.01, respectively), while that in salt lakes were the lowest (average Shannon and Chao1 were 1.96 and 184.84, respectively). With the increase of water salinity, the diversity and abundance of algal communities decreased significantly. The Average Variation Degree (AVD) index of algal community in different salinities lakes was different, and AVD in saline lakes was the lowest, indicating that the stability of algal community is the highest. At the phylum taxonomic level, the algae in the lakes of the QTP were mainly composed of Bacillariophyta (28.78%), Chlorophyta (14.28%), Euglenozoa (2.88%), Haptophyta (1.89%), including the species of uncultured_organism、Tetraselmis_cordiformis、Nannochloropsis_oculata、Rhizosolenia_sp. and the proportions were 31.94%, 9.06%, 6.30% and 3.58%, respectively. The community structure of algae in lakes with different salinities was significantly different (ANOSIM: P<0.001). Biological oxygen demand (BOD) was the most significant driving factor for variations in the community structure of algae in lakes with different salinities. Variational partition analysis (VPA) revealed that the contributions of geographic factors in shaping algae in lakes (1.02%) was lower than that of water environmental factors (36.95%). The algal community assembly process was varied in lakes with different salinity gradients. The community assembly processes of algae in fresh lakes were dominated by the deterministic processes, while the algae in saline and salt lakes were mainly dominated by the stochastic processes. The results of this study could provide theoretical support for the planning, utilization, and management strategies of water resources in lakes on the QTP, and also provided scientific basis for the assessment of water pollution risks in this region.