The sea breeze is a low‐frequency disturbance that severely damages the stability of small unmanned helicopters operating over the sea, especially for the yaw control, which is highly sensitive to disturbance. General internal model control is an appropriate method for dealing with this kind of operation conditions, whereas conventional internal model control cannot eliminate the tracking errors between a nominal model and a real model. In coping with unknown dynamics and low‐frequency gust disturbances for small helicopters, this paper proposes a novel robust controller constructed with system identification and integrator‐based improved general internal model. As a refinement of the conventional frame, the proposed control scheme extends the applicable scope of a controlled plant from a priori known dynamic to an unknown dynamic. Furthermore, under the proposed controller, it is guaranteed that the tracking error between the actual model and the nominal model converges to zero asymptotically. Finally, the effectiveness and advantage of the proposed control scheme are verified through comparative practical flight tests.