A linear trajectory tracking algorithm for tracking operation, could be used by the paddle boat for aquaculture. In order to cope with complex working environments, high-precision navigation must be adopted. The paddle boat could continue to be disturbed by wind and waves during the voyage. Interference could cause fluctuations in the track of the paddle boat. In order to realize high-precision navigation control of paddle boat and reduce influence of wind and wave interference, improve the stability of paddle boat process, save energy, reduce active frequency of the control system caused by the disturbance, and extend the duration of sailing and operation of paddle boat, a discrete sliding mode control method based on Kalman filter was proposed. Through the establishment of hydrodynamic model and yaw angle dynamic response model, the gain coefficient of discrete sliding mode control was designed and calculated. The negative feedback signal was denoised by two-dimensional Kalman filtering. After simulation verification and the actual boat was tested in the lake, and compared with the effect of PD control mode. As a result, the maximum overshoot was less than 25% of the PD control mode, the adjustment time was reduced by 50%, and the track deviation was less than 10cm. The discrete sliding mode control method based on Kalman filter achieved high-precision tracking of paddle boat, and the navigation process of paddle boat was more stable.