Mechanical stirring is one of the representative methods to mix and agitate the sludge inside a digester. It significantly affects the amount of biogas production by changing the number of propellers, the distance between the bottom and the propellers, and the distance between propellers and the operating cycle. Since the various factors affect the digester's efficiency, the optimal configuration of the mechanical agitators needs to be investigated in terms of the internal flow and turbulence structures inside the digester. We conducted a laboratory-scale digester experiment and Computational Fluid Dynamics (CFD) simulations, which both have the 40:1 scale, to find the optimal configuration of the digester located in Jeongeup, South Korea. The validity of the CFD model was verified by the comparison between the observation data taken from the laboratory experiment and the CFD results. Then, the flow velocity and the amount of sludge over time inside the digester, which has the actual scale, were numerically quantified by the verified CFD model. In addition, the position of the dead zone inside the digester depending on the different positions of the propellers was estimated. We confirmed that the array of the propellers significantly affects the flow structure and sludge sedimentation inside the digester.