Abstract: Abstract: Water pollution caused by the excessive growth of blue-green algae has become a growing environmental problem. One current approach to reducing the algae in Taihu Lake is to refloat the algae after a bloom has occurred. It can remove nitrogen and phosphorus in the lake simultaneously. The amount of algae-laden water collected from Taihu Lake can be up to approximately several thousand tons in wet weight per day. And they needs timely and effective treatment. The algae can be effectively degraded and produced into methane by anaerobic fermentation technology. The algae is easy to float and crust in the reactor, thus affecting the efficiency of the gas production and reducing the processing effect of the reactor. In anaerobic reactors, proper stirring can prevent algae floating and facilitate contact between the algae and other microbes, thereby improving gas production efficiency. This paper designed experimental device for optimizing the stirring of blue-green algae anaerobic fermentation. The device was made of double transparent glass with a working volume of 3 L. The device was equipped with an adjustable speed motor, which control the stirring interval, stirring duration and stirring cycle. Response surface methodology (RSM) was employed to optimize the stirring conditions. Simultaneously, the pilot study was adopted to provide a support of the best stirring condition of blue-green algae anaerobic fermentation. In the pilot study, protease content was assayed to characterize hydrolysis activity, TTC-dehydrogenase content was measured to characterize microbial enzyme activity, and coenzyme F420 content showed the activity of methanogenic anaerobes. The experimental results showed that the algae anaerobic fermentation was influenced by stirring interval, stirring duration, and stirring cycle. The correlation coefficient of the RSM regression equation was 0.98. RSM revealed the optimized stirring parameters for algae anaerobic fermentation as follows: Stirring intensity 56 r/min, stirring duration 20 min, and stirring cycle 6 h. Under these conditions, the proportional rates of gas and methane production in the pilot study were maximized at 0.39 and 0.236 L/(g·d), respectively. It was demonstrated that RSM methodology could be applied to the stirring process in larger-scale algae anaerobic fermentation reactors. Levels of protease, dehydrogenase, and coenzyme F420 were higher in optimized stirring parameters than other conditions. Stirring intensity was the main factor affecting biogas production by anaerobically fermenting algae. Stirring cycle exerted a secondary effect, while the effect of stirring duration was minor. Excessively intense and frequent stirring destroy the micro-environment of anaerobic microbial growth, partially disrupting the synergy between different anaerobic species. Conversely, an excessively weak stirring or prolonged stirring cycle lead to float of algae in the reactor, forming an upper algal layer. And the algal layer hinder the discharge of gas from the reactor. Meanwhile, less effective contact between algae and the microbes leads to the decrease of algae degradation rate.