In this paper, a variable damper is proposed to regulate the efficiency of a two-body wave energy converter (WEC) with mechanically driven power take-off (PTO). The variable damper introduces logic constraints into the WEC system, which can be translated into a mixed logical dynamical form with the dynamics of real-valued variables, the dynamics of logic variables, and their interactions. A hybrid model predictive control (MPC) method is used to determine the control inputs, which has the capacity to handle various constraints. The performance is assessed through simulations to evaluate the effectiveness of the proposed method. The achievable performance improvements of the proposed hybrid MPC are shown by means of comparative analysis with uncontrolled WEC devices. The results show that the proposed hybrid MPC has a high requirement on the lower bound of the variable damper and the maximum damping is used only at low relative velocities to achieve the optimum phase, like latching control. The hybrid MPC performs exceptionally well under wave conditions with a small significant wave height and long wave period, improving the power generation of the uncontrolled system up to 22.5%. And, the prediction error has a significant effect on hybrid MPC performance, especially for long prediction horizon.