Anthropogenic activities and climate change induce large-scale lake shrinkage in arid and semi-arid regions, threatening the structure of microeukaryotic communities. Despite their ecological importance, the diversity, drivers, assembly mechanisms, and ecological functions of these communities-especially pico-and nanoeukaryotes-are poorly understood. We conducted the first systematic study of pico-and nano-eukaryotic diversity, assembly mechanisms, and co-occurrence networks in Xinjiang's salinity-gradient lakes, offering new perspectives for understanding community dynamics in arid ecosystems. We collected 34 samples from five Xinjiang lakes and sequenced the 18S rRNA V4 region. Results revealed a U-shaped pattern in alpha-diversity for both pico-and nano-eukaryotes with increasing salinity, more pronounced in nano-eukaryotes. The two fractions differed significantly in beta-diversity across salinity levels. Redundancy analysis (RDA) identified salinity as the key environmental driver of community variation. Both communities were mainly structured by stochastic processes. Pico-eukaryotes exhibited more complex and modular networks, while nano-eukaryotes showed predominantly positive interactions. These findings enhance our understanding of climate impacts on microeukaryotic communities in arid lakes.