Taking the physical model of cylindrical biogas digester as the research project to design automatic flushing basin of biogas digester, the flow of the digester was rotated by designing feed pipe to be tangential. Fluent was used to analyze the process. It was found that the grit deposition area that was on lower left bottom. Based on the theory of hydraulic similarity, the design digester and the conventional digester were established. The angle between grit discharge pipe and feed pipe was designed for 150° according to the sedimentation law. Water was used as experiment fluid, whose sand contents were 10%. The results showed that sand would be collected at the 3rd discharging at design digester, the grit removal rate was up to 86.13% at the 5th, the average grit removal rate for 19 times was 3.81 times of the conventional, and the average of the 5th to 22nd was 82.17%. The grit removal result of conventional was exceeded by the design.