With the intensification of the world's energy demand, clean and efficient marine energy has received more attention, and the energy conversion device is particularly important. As an important part of the oscillating wave energy conversion device, the hydrodynamic characteristics of cylindrical absorbers have a great impact on the wave energy conversion efficiency. When the cylindrical buoys with different bottom configurations heave under the action of waves, the oscillating motion and flow field become more complex. At present, the potential flow theory is usually used to predict the motion response of cylindrical buoys in waves. Although the calculation speed is fast, there will be large errors due to the lack of consideration of the effect of fluid viscosity. To explore this error range, a three-dimensional numerical wave pool is established based on the viscous fluid theory and STARCCM+ software to study the response of the buoy and wave coupling action considering the viscous effect. At the same time, based upon the potential flow theory, the analytical solution of the cylindrical buoy oscillating in waves is established. Combined with the CFD numerical simulation results, the oscillation laws of the buoys with different bottom configurations in waves with different periods are compared, and the effects of viscosity on the buoys’ motion are also explored. According to the calculation results of floating buoy movement under viscous and non-viscous fluid, the statistical correction algorithm is adopted to obtain the viscous hydrodynamic correction algorithm of floating buoy movement based on the potential flow theory, and the feasibility is verified by viscous numerical simulation under other wave periods.