An experiment was conducted to evaluate the effect of natural and rapid decay of Microcystis aeruginosa bloom on the production of CH₄, and the variations of water environmental factors as well as the release fluxes of CH₄ and CO₂ were also explored. The results indicated that the dynamics of water environmental factors and gas production during the decay of dense Microcystis aeruginosa followed a similar temporal pattern, and algal decay significantly promoted the production of CH₄ and CO₂. The CH₄ cumulative release of natural decay and rapid decay were 22.80 and 37.72 times that of control group respectively, and the CO₂ cumulative release of natural decay and rapid decay were 5.36 and 4.03 times that of control group respectively. There was little difference in total carbon (C) release between natural decay and rapid decay. However, the proportion of CH₄ in the gas released from rapid decay was 1.86 times that of natural decay. The correlation analysis revealed that dissolved organic carbon (DOC) was the dominant environmental factor affecting the release of CH₄ and CO₂. Moreover, the aromatic protein and soluble microbial metabolites of DOC were the main substrates for CH₄ and CO₂ production.