<p>Ship-mounted cranes are vital for port logistics, but their operation faces significant challenges due to external disturbances such as sea winds and waves, as well as the inherent underactuated dynamics of the system. To address these challenges, this paper proposes an advanced anti-swing control scheme that integrates a configurable observer with backstepping control. The configurable observer dynamically adjusts its structural configuration based on the type of controller and employs an optimal control strategy to set its observation gain, thereby providing accurate state and disturbance estimates. The backstepping control algorithm, which is applicable to underactuated systems, leverages these estimates to overcome the reliance on precise models, achieving precise positioning and swing suppression. The observer and controller are structurally integrated and complementary in terms of modeling, enabling real-time estimation of external disturbances and effective control of the underactuated ship-mounted crane system. Experimental results demonstrate the enhanced crane stability and efficiency in complex port environments, thereby advancing port logistics performance.</p>