In this paper, we investigate the tracking control problem of a hovercraft vessel with uncertainties via a fuzzy gain scheduled integral control. There are two parts in this paper: the simulation and the experiment. In the first section, we will apply PID control as well as the proposed control law in the hovercraft system. Simulation results reveal that the proposed control scheme is promising for controlling uncertain hovercraft systems. In experimental part, we use the Complex Programmable Logic Device (CPLD) to realize the PID controller. Because of the mature development and easy acquirability of CPLD, we digitize this controller and develop it by the Altera CPLD platform. The peripheral circuit and the controller are established in our new system on a chip. It can shorten the time for manufacturing electronic circuits, and can also achieve the goal of a fast prototype. In addition, the implementation cost decreased significantly by this scheme.