The payload often experiences unpredictable motion due to the combined effects of random waves and wind loads, significantly impacting the safety and efficiency of offshore operations. To expand the effective working window for offshore transfer operations, this study introduces a multi-cable payload transfer system (MPTS). Using a 45-ton offshore crane mounted on a multipurpose vessel from COSCO Shipping Group as a prototype, this study establishes a dynamic model of MPTS, considering the effects of vessel motion, crane actions, and wind loads. The payload remains in an unstable state due to external disturbances. Additionally, variations in payload specifications and mass lead to considerable uncertainties in the dynamic parameters of MPTS. To address these uncertainties, a second-order linear observer is developed. Subsequently, an improved computed torque controller is proposed, and the boundedness of the tracking errors is proven using the Lyapunov theory. The transfer process is divided into three distinct phases: lifting, slewing, and lowering. The feasibility of the transfer scheme is verified through high-fidelity simulations and prototype experiments. This research provides a solid theoretical foundation for the subsequent engineering application of MPTS.