Effects of incident wave angle and complicated topography on hydrodynamic characteristics of a buoy are studied using the Finite Element Method (FEM). The hydrodynamic coefficients of different conditions are acquired. The correctness of the numerical method is verified through a comparison with analytical results of a simple seabed. In order to improve the efficiency of the analysis, the BiCGStab algorithm, considered to be among the most powerful algorithm in solving linear systems, is employed. The results presented here will supply some important information for designs of ocean structures.