Ocean wave induced vessel heave motion is one of the most important issues in marine operation, especially in the load transfer using overhead crane system. The control of marine overhead crane system aims to regulate the positioning of the cart and the payload continuously, irrespective of the vessel heave motion. This paper presented an integrated motion controller by incorporating the active heave compensator into the winch classical PID motion controller. Through active heave compensator, the gap between the payload and the vessel main deck was continuously monitored and regulated to avoid hammering of the payload into the intended mating object. From the simulation results, the performance of the overhead crane system, assisted by the integrated winch PID motion controller and active heave compensation mechanism, can be significantly improved, even in the presence of ocean wave induced vessel heave motion, with distinctively small payload sway angle and displacement errors.