For the problems of SWATH ship motions with external disturbances and parametric uncertainty, the nonlinear predictive control with the disturbance observer is proposed for SWATH ship motions. The SWATH ship motion model is built, hydrodynamics are got, and wave disturbances are learned firstly. Then the nonlinear predictive control law is designed for SWATH ship heave and pitch motions. And the disturbance observer is used to observe wave disturbance of SWATH ship. It is theoretically proved that the proposed controller can ensure the stability of SWATH ship motions. Simulation results show that the designed controller can get better performance of SWATH ship motions, also wave disturbances can be restrained.