With climate change and intensive human activities, eutrophication of global lakes is increasing. Cyanobacteria blooms occur frequently in lakes. Lakes are the hot spots of global carbon cycle. On one hand, carbon dioxide (CO₂) is fixed in the atmosphere through photosynthesis of phytoplankton. On the other hand, CO₂ and methane (CH₄) are emitted into the atmosphere through the degradation of organic matter. Current research on the effect of cyanobacterial bloom on carbon source and sink mainly focused on the effect of algae death and degradation on carbon-containing greenhouse gas emissions. There are few studies on the photosynthetic carbon sequestration effect of algae. Therefore, surface sediments effects of cyanobacterial blooms in lakes are not clear. In this study, surface sediments were collected from Zhushan Bay, Lake Taihu in summer of 2023 to form a sediment-overlying water system. By adding different biomass of cyanobacteria, indoor constant temperature water bath culture simulation experiments were conducted. The concentrations of CO₂ and CH₄ and the abundance of carbon isotope in the headspace were measured by sampling in the culture columns. Effects of cyanobacterial bloom's growth and decline on CO₂ and CH₄ production pathways and emission fluxes were studied. The results showed that cyanobacteria growth and decay correspond to CO₂ absorption and emission states, respectively. The CO₂ emission flux increased with adding of initial cyanobacterial. The CO₂ emission flux was negative in the growth stage of cyanobacteria as algae fixed the CO₂. CO₂ emission flux during the decay stage increased gradually with the death and decomposition of cyanobacteria. It reached to stability on the 25th day. CH₄ emission flux in the growth stage was (0.022±0.011)-(3.159±0.51) μmol/(m²·h) reaching its peak on the 7th day. CH₄ emissions during the death stage increased significantly, reaching (0.219±0.017)-(9.783±0.215) μmol/(m²·h) with a peak on the 20th day. After converting CH₄ to CO₂ equivalent (CO₂-eq) and summarizing, the total CO₂-eq of each group showed as a “carbon sink” (-451.82--113.28 mmol/(m²·h)) during the whole experiment. However, it was a “carbon source” (35.46-196.86 mmol/(m²·h)) during the death stage. The net CO₂-eq emission flux during the whole experiment period was -746.71 mmol/(m²·h), the water columns displayed a strong carbon sink effect. The results of ¹³C-CO₂ and ¹³C-CH₄ stable isotopes showed that the apparent fractionation factor α_C were less than 1.06. It indicated that acetic acid fermentation was the main pathway of CH₄ production in both growth and decay stages of cyanobacteria. α_C gradually decreased with the increase of initial cyanobacteria supplement. This result indicated that cyanobacteria increased the proportion of acetic acid fermentation pathway in CH₄ metabolism. These findings have important scientific significance in revealing the mechanism of cyanobacterial blooms on carbon cycling and source sink effects in eutrophic lakes.