Flying boat is a fixed-wing airplane capable of landing and taking off on water, and its performance, evaluated by its sea-keeping ability, strongly depends on sea conditions. A Flying boat with good sea-keeping ability can reduce impacts from waves and runs safely and smoothly under a certain sea state. However, sea-keeping ability is still the key problem that hinders its development and application. In this paper, based on the mathematical model of a flying boat, a simulation system predicting the motions of the flying boat on an irregular wave is built, and a controller deduced by active disturbance rejection control (ADRC) and Tagaki-Sugeno (T-S) fuzzy reasoning is applied to improve the sea-keeping ability. The simulation results show that the flying boat has good performances for tracking the surface of waves, reducing impact from water, and making the flying boat take off on three water conditions safely (calm water, water with regular wave and water with irregular wave respectively).