The control system is one of the important components of the hydrofoil craft. By adjusting the navigation attitude of the craft, the hydrofoil craft can navigate stably and safely in the turbulent environment. Aiming at the problem that existing control algorithms have poor stability in the longitudinal motion control of hydrofoil craft, the longitudinal motion reduction is limited, and there are excessive requirements for accurate disturbance wave data. Based on the fully submerged hydrofoil craft model, this article proposes a joint control method LQRY-SMC combining linear-quadratic optimal control with output regulation (LQRY) and sliding-mode control (SMC), and adds genetic algorithm to optimize the weighting matrix parameters, get better control-feedback gain, improve the global optimal-control stability, thus improving the comfort of the crew, and prevent the attack of the hull, deck wetness and damage to instruments. The simulation results show that compared with the existing methods, the heave displacement and pitch angle obtained by LQRY-SMC under the turbulent flow of different significant wave heights are reduced by about 50%, and the influence of longitudinal motion on hydrofoil crafts is avoided to a large extent, which proves the effectiveness and superiority of the method proposed.