Abstract: As the largest shallow lake in the Yellow River basin, Ulansuhai Lake is characterized by periodic blooms of Huangtai algae, which have become a prominent indicator of ecosystem degradation. This study focused on the microbial community characteristics, functional mechanisms, and potential risks of Huangtai algae. Using metagenomic sequencing, co-occurrence network analysis and redundancy analysis (RDA), we systematically analyzed its species composition, functional characteristics, algae-bacteria interaction patterns, and environmental response mechanisms. The results showed that bacteria were the absolutely dominant group (accounting for more than 98%), with the core dominant phyla being Cyanobacteriota, Pseudomonadota, and Bacteroidota, while eukaryotic microalgae accounted for less than 1%. The community structure showed obvious successive changes: Cyanobacteriota accounted for 66.8% at the initial bloom stage (May); the relative abundances of Pseudomonadota and Bacteroidota increased significantly at the middle stage (July); and Planctomycetota became the dominant at the late stage (September). RDA showed that community structure was significantly correlated with environmental factors such as water temperature and nutrients (the first two axes explained 84.23% of the total variation). Functional annotation indicated that the biosynthesis of other secondary metabolites (ko01110) was significantly enriched, and the total contribution rate of Cyanobacteriota, Pseudomonadota, and Bacteroidota to functional characteristics reached 88.26%. Co-occurrence network analysis revealed that algae-bacteria interaction was the core driving mechanism for the continuous outbreak of Huangtai algae. The staged succession of functional modules and keystone nodes supported the whole life cycle of the algal community, with ko01110 as the key functional pathway throughout. Huangtai algae blooms also pose multiple potential risks to the aquatic ecosystem. This study clarifies the mechanism of Huangtai algae blooms from a microbiological perspective and provides a theoretical basis for the ecological control of filamentous algal aggregates in shallow eutrophic lakes.