Abstract: To address the dual challenges of excessive Phragmites australis biomass accumulation and the chronic shortage of external carbon sources for wastewater treatment, this research developed a coupled process involving alkali-thermal pretreatment and microbial fermentation. Reeds were harvested from the experimental site at the Dongting Lake Station for Wetland Ecosystem Research (29°19′49″N, 112°59′02″E) on April 15, 2023. To ensure homogeneity, dry aboveground stalks from the previous year were crushed into fragments approximately 1 cm in length. The study employed a two-stage experimental design. In the first stage, reeds were subjected to alkali-thermal modification using varying concentrations of NaOH (1%, 2%, and 5%) at 60 °C for a 24 h immersion period. In the second stage, the resulting residues were utilized in solid-state fermentation at 35 °C for 18 days, inoculated at 0.2% (v/w) with four microbial agents: Bacillus licheniformis, Aspergillus niger, Trichoderma harzianum, and effective microorganisms (EM) composite bacteria. The study systematically evaluated the impact of these treatments on total organic carbon (TOC) release and the control of secondary total nitrogen (TN) and total phosphorus (TP) pollution. The research results indicated that the 5% NaOH treatment group achieved the highest average TOC release concentration (1 338.49 mg/L), and its cumulative release of total nitrogen (TN) and total phosphorus (TP) was significantly lower than that of the 1%NaOH treatment group. EM composite bacteria exhibited the optimal synergistic performance in carbon release and nutrient immobilization. Its cumulative TOC release (279.44 mg) was approximately 4.1-4.6 times that of the single-strain groups, and the secondary release of nitrogen and phosphorus was significantly inhibited through microbial bio-assimilation. Within the concentration range set in this study, the coupling of 5%NaOH alkali-thermal pretreatment and EM composite fermentation represents the optimal process for preparing reed-based organic carbon sources from Dongting Lake, providing a theoretical foundation for the high-value utilization of wetland plants. In the microbial fermentation stage, the EM composite bacteria demonstrated superior performance in synergistic carbon release and nutrient immobilization compared to the three single-strain treatments. Furthermore, the EM group maintained TN (0.14 mg) and TP (0.009 mg) cumulative release at levels 90%-99% lower than other strains. This is primarily due to the stable symbiotic system of EM bacteria, including photosynthetic bacteria, lactic acid bacteria, and yeasts which enhances the enzymatic degradation of lignocellulose through interspecific synergy. Moreover, the vigorous ‘biological pump’ effect of the EM consortium allowed for the active assimilation of dissolved nitrogen and phosphorus into microbial biomass, effectively achieving ‘near-zero release’ of these pollutants. In conclusion, within the parameters of this study, the combination of 5% NaOH alkali-thermal pretreatment followed by EM composite bacteria fermentation is the optimal process for preparing high-quality reed-based organic carbon sources. This integrated technology overcomes the traditional barriers of lignocellulose recalcitrance and secondary pollution risks, providing a theoretical basis for the high-value resource utilization of Phragmites australis and offering a sustainable, green alternative for carbon source supplementation in wastewater treatment.