Under the context of global warming, the Qinghai-Tibet Plateau has given rise to diverse glacial lakes, with glacier retreat influencing microbial community composition and distribution in these lakes by altering aquatic environmental conditions. Investigating the heterogeneity of unique algal communities and their assembly mechanisms across different glacial lake types is crucial for understanding eukaryotic phytoplankton distribution patterns and their responses to environmental changes in the Tibetan Plateau"s glacial lakes. This study examined 10 glacial lakes in the Kuoqionggangri Glacier region of the southern Qinghai-Tibet Plateau, classifying them into proglacial lakes, glacier-fed lakes, and non-glacier-fed lakes based on meltwater supply patterns. Using 18S rDNA amplicon sequencing, co-occurrence network analysis, and community assembly modeling, we assessed how different water supply modes affect eukaryotic phytoplankton communities. The results revealed that Chlorophyta dominated these glacial lakes, with proglacial lakes exhibiting the highest α-diversity, stable community structures, and assembly processes primarily driven by dispersal limitation. In contrast, glacier-fed lakes displayed fragmented community structures shaped mainly by heterogeneous selection, while non-glacier-fed lakes had the lowest α-diversity, relying on strong species interactions for stability, with stochastic processes dominating community assembly. Water conductivity and total dissolved solids significantly influenced α-diversity, whereas nutrients had limited effects. These findings highlight the heterogeneity among glacial lake types in species composition, α- and β-diversity, community stability, assembly mechanisms, and environmental relationships, providing key insights into microbial community dynamics and ecological responses to environmental changes in high-altitude glacial lake ecosystems.