Summary The swing characteristics of the load of ship‐mounted rotary cranes is very complicated, due to the rotation of the boom. Especially, when the crane is operating at sea, it is subject to some disturbances caused by waves, which makes the precise control of the load more difficult. We study the control problem of a four degree of freedom ship‐mounted rotary crane with continuous yaw and roll disturbances in this paper. Specifically, we propose an adaptive controller and the adaptive laws can be updated in real‐time depending on the state of the system and the disturbance. This method does not require linearization of the crane dynamic equations, therefore, the crane can get great control performance even if it is far from the equilibrium point. Comparative experiments demonstrate that the proposed method has excellent anti‐disturbance ability.