Dual marine lifting systems are complicated, fully actuated mechatronics systems with multi-input and multi-output capabilities. The anti-swing cooperative lifting control of dual marine lifting systems with dual ships’ sway, heave, and roll motions is still open. The uncertainty regarding system parameters makes the task of achieving stable performance more challenging. To adjust both the attitude and position of large distributed-mass payloads to their target positions, this paper presents a time-delay-based sliding mode-tracking controller for cooperative dual marine lifting systems impacted by sea wave disturbances. Firstly, a dynamic model of a dual marine lifting system is established by using Lagrange’s method. Then, a kinematic coupling-based cooperative trajectory planning strategy is proposed by analyzing the coupling relationship between the dual marine lifting system and dual ship motion. After that, an improved sliding mode tracking controller is proposed by using time-delay estimation technology, which estimates unknown system parameters online. The finite-time convergence of full-state variables is rigorously proven. Finally, the simulation results verify the designed controller in terms of anti-swing control performance. The hardware experiments revealed that the proposed controller significantly reduces the actuator positioning errors by 83.33% compared with existing control methods.