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.