Retrieving Autonomous Underwater Vehicles (AUVs) using Unmanned Aerial Vehicles (UAVs) presents significant challenges due to wave-induced motion and wind disturbances during recovery. While prior research has primarily addressed air-to-air refueling and ground-to-air deployments, this work introduces an eagle-inspired UAV trajectory generation and control system specifically designed for AUV retrieval. Drawing inspiration from avian flight dynamics, the proposed approach mitigates the effects of downward airflow and environmental disturbances, enabling a stable and efficient recovery process. We propose a novel trajectory planning method that minimizes snap, integrates a cost function to account for the UAV’s airflow effects on the target, and adapts dynamically to wave-induced movements. A specialized connection mechanism, consisting of a hook-equipped UAV and a buoy-rope assembly attached to the AUV, is developed and validated through reduced-scale in-water field experiments. Post-connection, a suspended load controller ensures stability by compensating for shifts in inertia and external forces. Additionally, we present a Unity-based simulation environment that allows customization of vehicle parameters and mission scenarios. This work bridges the gap in maritime operations, offering a reliable and flexible solution for AUV recovery in dynamic marine environments.