A ride control system (RCS) based linear quadratic regulator (LQR) and genetic algorithm (GA) design is presented, to reduce the heave, roll and pitch motion (three degrees of freedom motion (3 DOF motion)) of the wave piercing catamarans (WPC) in beam waves. A detailed 3 DOF ride control model which consists of the coupling and decoupling relationships between longitudinal and transverse motion is proposed for the WPC vessel. And the complex hydrodynamic coefficients and disturbances induced by beam waves are analyzed. Moreover, two stern flaps are designed for the system in the way of alternate flapping. In the controller design, the LQR method based on GA method is adopted to reduce the 3 DOF motion of the ship. Depending on the robust search mechanism and global optimum of GA, weighting parameters can be obtained to calculate the desired gain. Finally, the motion reduction and motion sickness incidence (MSI) results demonstrate the feasibility and effectiveness of the proposed controller, and the comfort of passengers and crews can also be improved.