As a special airplane, a flying boat can take off from water and land in water, which makes its controller design more complicated than that of other general airplanes. Based on the mathematical model of a flying boat, two controllers applying classical PID (Proportional Integration Differential) method and a compound control method (combining active-disturbance rejection controller (ADRC) and dynamic inversion (DI) methods) are designed respectively. Then the performances of the two controllers are validated by tracking a speed step signal from 15m/s to 16m/s in clam water, holding the speed and the pitch angle of the flying boat in water with regular waves, and taking off from water with and without waves. The results of the simulations show that the controllers can improve the stability and seakeeping quality of the flying boat.