To investigate greenhouse gas flux on the water-air interface in autumn, the large enclosures were built up in the near-shore zone of the northwestern Lake Chaohu, China. The YL-1000 large-scale bionic cyanobacteria removal equipment was used to salvage cyanobacteria in situ. The characteristics of CH₄ and CO₂ fluxes and their influencing factors in the salvaging and control zone were observed by static chamber method equipped with a portable greenhouse gas analyzer. The results showed that the concentration of chlorophyll-a and suspended solids (SS) (29.6±2.5 μg/L and 12.5±1.2 mg/L, respectively) in the salvaging zone significantly decreased with the reduction rate of 72% and 85%, respectively, compared with those in the control. The removal of particulate matter like total nitrogen, total phosphorus, SS and COD_Mn after salvaging was effective. The microbially-derived humic-like (C1) and autochthonous protein-like (C3) components in the DOM significantly decreased during the salvaging process. The C1 and C3 fluorescence intensity (0.18±0.02 RU and 0.06±0.01 RU, respectively) in the salvaging zone were significantly lower than those of control (0.26±0.05 RU and 0.12±0.03 RU, respectively), which suggested that salvaging can effectively control the release of algal-derived dissolved organic matter. The average flux of CH₄ in the control (17.473±1.514 nmol/(m²·s)) was twice than that of the salvaging zone (7.004±4.163 nmol/(m²·s)). In the salvaging zone, CH₄ flux was significantly positively correlated with Chl.a, C1 and C3 components, which suggested that algal-derived organic matter could promote CH₄ flux. The CO₂ flux showed a significant upward trend in the salvaging zone and remained constant in the control. The CO₂ flux (-0.200±0.069 μmol/(m²·s)) in the salvaging zone was significantly higher than that in the control (-0.344±0.017 μmol/(m²·s)). The CO₂ flux was significantly negatively correlated with Chl.a and temperature in salvaging zone. The total greenhouse gas emission reduction for CH₄ and CO₂ is 0.275±0.076 mol/(m²·d) (carbon dioxide equivalent). The results reveal that the continuous cyanobacterial salvaging process in Lake Chaohu reduces the flux of greenhouse gas on the water-air interface, and can slow down the vicious cycles between cyanobacterial blooms and lake eutrophication and climate warming.