A new second order sliding mode control algorithm is proposed for nonlinear system of the ship course-keeping control subject to input saturation in the presence of model errors and external disturbances. The controller is constructed by combining backstepping technique and second order sliding mode control, which is not only capable of strengthening robustness of the system and improving its accuracy, but can also effectively attenuate inherent chattering of classical sliding mode control. Meanwhile, an input internal compensation saturation auxiliary system is used to deal with input saturation limitation of course control system. An innovative neural network compensator is designed to completely counteract effects of the modeling errors and the effect of the external disturbances are addressed by using the property of hyperbolic tangent function. The results of simulation show that the designed controller guarantees that all the close-loop signals are uniform ultimately bounded and the course error converges to a small neighborhood of the desired course.