In order to explore the effect of enriched organic matter in eutrophic shallow lakes on water quality and carbon cycle, in this study, we constructed a microcosm system to simulate the separate decomposition and mixed decomposition of cyanobacteria and reed debris. The changes of nutrient concentration, organic matter content and structure of the overlying water in each treatment were determined to reveal the release characteristics of nutrients and organic carbon during the mixed decomposition process of cyanobacteria and reed debris in eutrophic lakes. The results showed that the total carbon (TC) release of the mixed treatment was significantly higher than the theoretical value within 0-88 hours of the experiment under the same carbon source addition, indicating that there is a co-metabolism effect during the mixed decomposition of cyanobacteria and reed debris. In the initial stage of the cultivation, sediments accelerated the release of total nitrogen (TN) and total phosphorus (TP) to the overlying water and caused a significant impact on the water quality via the co-metabolism effect. Compared with the reed treatment, the maximal release of TN and TP in the mixed treatment increased by 13.49% and 26.84%, respectively. The change of fluorescence intensity of fulvic acid characterized by the three-dimensional fluorescence spectroscopy (EEMs) also showed that the decomposition rate of reed was faster in the mixed treatment group. At the beginning of cultivation, each treatment quickly turned into anaerobic state, and the concentration of TC, TN and TP displayed a trend of dramatical increase and then gradually flattened, with a maximum of (372.4±2.98), (138.45±2.97), and (7.95±1.11) mg/L at 228, 108 and 324 hours, respectively. The variations of bacterial specific fatty acid showed that the input of Microcystis detritus into Phragmites detritus increased the abundance of decomposing bacteria in Phragmites detritus, and accelerated the decomposition rates, resulting in the co-metabolism of Microcystis and Phragmites carbon. Under the background of global warming, with the increasing frequency of algae outbreaks in eutrophic lakes, the co-metabolism effect may be further strengthened, and the water quality of eutrophic lakes will be affected continuously.