To address the problem of lignin membrane fouling caused by dynamic cross-flow in the process of retaining and concentrating the black liquor byproduct of papermaking, this paper uses three different rotating structures (vane, disk and propeller) to increase the surface shear force and filtration flux of the membrane. In this paper, under different rotating speeds and different transmembrane pressure differences, numerical simulations were conducted on the shear forces generated by the three structures and the retention process on the surface of the membrane. The variation laws were also studied and compared. Under the same filtration conditions, the vane structure demonstrates better results than the propeller and disk structures in terms of increasing filtration flux. Based on the result, the vane shear force was simulated in terms of changing the particle deposition, and compared with vane rotating speeds of 100–700 r/min, the surface particle deposition of the membrane was significantly reduced at a rotating speed of 800 r/min. Finally, the numerical simulation results were experimentally validated to ensure the accuracy of the simulation. The findings provide a theoretical basis and practical value for solving the problem of lignin membrane fouling caused by dynamic cross-flow in the process of retaining and concentrating the black liquor byproduct of papermaking.