Designing ship controllers is a challenging problem because of nonlinear dynamics, uncertainty in parameters and external disturbances. Furthermore, the interaction between yaw and roll angles increase the complexity of this issue when autopilot and roll stabilizer are considered together. In this research, a MIMO sliding mode controller is designed to control yaw and roll angles simultaneously. The major contribution of the paper is designing an integrated controller based on a nonlinear model of ship as well as considering analytic bounds of uncertainties. Then, in order to reduce the chattering phenomenon and to improve the tracking ability of the system, the control scheme has been modified using an integral switching variable. Simulation results show the success of the proposed method to overcome nonlinearity and disturbances, as well as high performance in rough wave conditions. Also, comparison between the proposed controller and two SISO control schemes demonstrates advantages of the integrated control method.