Based on flow mathematical model and mathematical model of ship navigation, a plane 2-D mathematical model of ship navigation manipulation is established, which is under the body-fitted coordinate system based on staggered grid, which is perfect for inland rivers. The flow mathematical model uses the 2-D flow mathematical model which is under the body-fitted coordinate system based on staggered grid, and the ship navigation model uses the combination-type hydrodynamic model. Based on the checking test in still water and regular flow, through the simulation on ship manipulation in complicated flow, we get that the 2-D mathematical model of ship navigation manipulation can basically simulate the ship navigation in complicated flow.