Trajectory tracking plays a notable role in unmanned surface vehicles (USV), especially for the emerging intelligent aquaculture, as the level of integration, high-efficiency, and low-labor-intensity of such USV is determined by trajectory tracking. Here, we report a generic trajectory tracking control system for a paddle boat by establishing a three-degree-of-freedom kinematics model, which could precisely characterize the relationship between velocities, forces and moments of the paddle boat. A Pixhawk 4 as the core controller of the hardware system could be integrated with the other hardware submodules and could complete the wireless data transmission, monitoring and remote control functions. Meanwhile, we establish a fuzzy rule table, consider the advantages of line-of-sight (LOS) guidance and fuzzy adaptive proportional-integral-differential (PID) algorithm, combine the two parts and apply them as the key algorithm in the trajectory tracking of the paddle boat. Demonstrations include trajectory tracking effect at different velocities, turning effect at left-turn moment, and trajectory tracking effect at different turning angles. The results show that the paddle boat is able to travel under the trajectory formed by following the planned waypoints within the error allowed, which is called effective trajectory tracking. And can offer an alternative pathway toward achieving effective trajectory tracking control in advanced intelligent aquaculture USV for smartly and wirelessly operated pond drug spraying.