To solve the ship course control problem with nonlinear terms, input saturation, and complex noise, this paper proposes a saturated ship course control method with complex noise based on generalized fuzzy hyperbolic model (GFHM). Due to the characteristics of fewer identification parameters, GFHM can simplify the complexity of traditional ship fuzzy models. GFHM is more suitable for multi-variable nonlinear systems such as ships of which variables are limited and difficult to measure. Furthermore, to deal with the input rudder angle saturation problem caused by the limited capability to compensate the shipboard equipment controller, an auxiliary system is proposed. And the complex noise in the navigation environment is described by the random process. Then, a new type of ship fuzzy course controller is designed based on the theoretical framework of random differential equations (RDEs) and it is proved that the ship course system under the proposed GFHM-based controller is noise-to-state stable in probability (NSS-P) and the state is an asymptotic gain in probability (AG-P). The simulation results show that the proposed algorithm in this paper can effectively control the ship’s course.