Abstract Algal blooms significantly affect microbial communities in wetland ecosystems. However, little is known about the succession of sediment microbial communities during algal blooms. This study aimed to investigate the temporal patterns of sediment bacterial community structure and function succession during algal blooms (March to May 2022) with high-throughput sequencing technology. To this end, algal blooms were divided into the bloom stage (BS), decomposition stage (DS) and end stage (ES). The results showed that: (i) The algal blooms were dominated by Microcystis species within Cyanobacteria. Both phytoplankton abundance and biomass reached the peak in the BS, with 45.78 × 105 cells/L and 5.97 mg/L, respectively. (ii) The alpha diversity indices of the sediment bacterial community showed a monotonically increasing trend, with the lowest value in the BS. Cyanobacterial blooms reduced the relative abundance of Actinobacteria and Chloroflexi, and raised that of Firmicutes, Proteobacteria and Bacteroidetes. (iii) Cyanobacterial blooms remarkably decreased the complexity of the co-occurrence network of the sediment bacterial community, which resisted extreme environmental conditions in the BS and DS by increasing positive relationships. (iv) Mantel test showed that phytoplankton biomass, T, dissolved oxygen and organic carbon had significant effects on the sediment bacterial community. The results of this study are important for the ecological management of algal blooms through microorganisms.