The theoretical method, or named the potential flow method, is most widely used in the research of maneuvering in waves. However, this approach used in previous studies is based on the assumption that maneuvering hydrodynamic derivatives in waves are the same as those in calm water. However, this assumption can be inaccurate, which makes the simulations different from the experimental results sometimes. Meanwhile, there are few experiments performed to investigate the hydrodynamic derivatives in waves considering the complexities of the experimental setup and data processing. There is even no systematic numerical simulation in this field. Considering the importance of the wave effect on the hydrodynamic derivatives and the advantages of the computational fluid dynamics (CFD) method, in this study, the numerical simulations of the planar motion mechanism (PMM) tests on a containership S175 in regular waves are performed systematically for the first time. The hydrodynamic derivatives in waves of the target model are obtained by simulations in following waves, to be specific, the surf-riding condition. The surf-riding condition is chosen for separating the wave-induced component easily and researching the reason for the broaching-to phenomenon. The simulation results are validated by experimental data with satisfactory accuracy, which indicates the effectiveness of the numerical setup. The results reveal that the wave has a significant effect on hydrodynamic derivatives. The detailed changing trends and simulation methods of all hydrodynamic derivatives are proposed in this paper. Moreover, the course stability in waves is evaluated by the hydrodynamic derivatives in waves, which verifies the reason for the occurrence of the broaching-to phenomenon.