Organic matter degradation in shallow lake sediments is a key process in regulating the carbon cycle and greenhouse gas emissions, while the mechanism by which submerged plant residue degradation regulates the long-term succession of microbial communities has not yet been clarified. [Objective] To investigate the mechanisms of microbial community succession driven by submerged plant residue degradation on long time scales. [Methods] We investigated the degradation dynamics of Potamogeton wrightii residues in Taihu Lake sediments through a 4-year microcosmic simulation experiment and analyzed in detail the dynamic impacts of organic matter fraction evolution and extracellular enzyme activities on microbial community succession. [Results] The rapid consumption of labile organic matter pool was accompanied by a surge in β- glucosidase activity, while the accumulation of recalcitrant organic matter pool was coupled with a lagged response of phenol oxidase activity. Microbial communities showed significant functional differentiation, with Bacillota and Basidiomycota dominating the degradation of recalcitrant organic matter pool in bacterial and fungal communities, respectively, revealing the metabolic division of labor in the degradation of lignin-like polymers. Variance decomposition showed that both labile and recalcitrant organic matter pools independently explained microbial community variations, highlighting the role of chemical complexity of organic matter in screening functional taxa. [Conclusion] Degradation of submerged plant residues significantly drove microbial community structure succession in the microcosmic culture system, and microbial community composition and organic matter fractions showed synergistic changes. In addition, the degradation promoted the growth of microorganisms with different growth strategies. This study elucidates the dynamic interactions between microbial functional differences and organic matter pool complexity in the degradation of submerged plant residues, providing a theoretical basis for carbon stability assessment and ecological restoration of shallow lakes.