This paper presents a two-time scale control structure for the course keeping of an advanced marine surface vehicle, namely, the fully submerged hydrofoil vessel. The mathematical model of course keeping control for the fully submerged hydrofoil vessel is firstly analyzed. The dynamics of the hydrofoil servo system is considered during control design. A two-time scale model is established so that the controllers of the fast and slow subsystems can be designed separately. A robust integral of the sign of the error (RISE) feedback control is proposed for the slow varying system and a disturbance observer based state feedback control is established for the fast varying system, which guarantees the disturbance rejection performance for the two-time scale systems. Asymptotic stability is achieved for the overall closed-loop system based on Lyapunov stability theory. Simulation results show the effectiveness and robustness of the proposed methodology.