As an important structure for utilizing wave energy, the two-body floating point absorber (FPA) wave energy converter has a simple structure, high energy conversion rate, and wide frequency response range. In this paper, a heave motion model of two-body FPA wave energy converter was established. On this basis, the secondary development of AQWA software programming in Fortran language was conducted by reckoning in the power take-off (PTO) effect, and the motion simulation of the two-body FPA wave energy converter was realized. For the specific oscillating two-body FPA model, the study analysed the frequency domain hydrodynamic performance and the time domain motion characteristics of the device. The results showed that the numerical model was adequate to predict the motion performance of the two-body FPA. The maximum value of the heaving response amplitude operator (RAO) was reached with the frequency of 0.7–0.8 rad/s. As the wave period increased, the generated power of the two-body FPA initially increased and subsequently decreased. The stiffness coefficient has less effect on the generated power than the damping coefficient. The results and conclusions have reference significance for the development of new wave energy devices and the efficient and reliable utilization of wave energy.