The efficient stirring is crucial for mixing anaerobic bacteria and substrate in a Continuous Stirred Tank Reactor (CSTR). In this study, we propose a CFD model (Large Eddy Simulation (LES) model) to simulate the reactor’s flow characteristics. The standard turbine paddle modes of the CSTR with different shafts and paddle layers were investigated using XFLOW software. The simulation results reveal that the quantity of shafts and layers has significant influences on the flow characteristics of the reactor. Both single-shaft and double-shaft paddles can provide a complete circulation loop. The mixing performance of single-shaft paddles surpasses that of double-shaft paddles. Moreover, the double layer paddles have better mixing performance than the single layer paddles. Therefore, the most favorable paddle mode for a CSTR is the single shaft paddles with double layers.