As a lubrication medium, the shaft-seal water often carries substantial sand particles in the cutter suction dredger, causing severe wear and tear of the internal components of the slurry pump. It has been proved that the shaft seal water system could be optimized by introducing a hydro cyclone to prolong the service life of the slurry pump. However, it was found that the seasonal variation of water viscosity would produce an obvious effect on the centrifugal separation of sand particles. Therefore, in this study, the influence of seasonal viscosity change on the flow field characteristics and sand particle separation was systematically studied by computational fluid dynamics (CFD). The simulation results showed that the fluid and pressure field in hydro cyclone has good symmetry under different viscosity. While with the increase of viscosity, the fluid resistance coefficient increases, resulting in a downward trend of turbulent kinetic energy and an upward trend of negative pressure zone, which is not conducive to sand particle separation. Moreover, to verify the consistency between simulation and actual industry, the grade efficiency of sand particles was studied and discussed. The average particle size of sand could be reduced from 37.8 μm to 8.1 μm, and the separation efficiency could reach 90% under better suitable dredging conditions (Salinity: 34%, Temperature: 20 °C). Further, the experimental and industrial results showed that the fish hook effect inevitably existed in practice due to the entrainment of coarse particles. This study would provide theoretical support for the subsequent optimization of the shaft seal water system.