The new position control scheme at the terminal time in 3-D space is proposed for mobile harbor (MH) crane system equipped with a dual-stage trolley and hoist. Wave-induced motions of the MH and container ship cause swing of the payload and time-varying target position. Since the payload being applied by resonant disturbances should be loaded or unloaded on the moving container ship with resonance frequency, it is the worst environment to perform the accurate position control. In the proposed control method, the payload is only matched to the target at the terminal time unlike the tracking control approach which makes the payload to follow the movement of target on whole time. The terminal time is defined as the moment that the target velocity is minimum to prevent damage of the container. And this method is composed of swing free control stage and positon control stage. Control schemes in each stage are model-based optimal control. To discuss the efficiency of the proposed position control, numerical simulations results and performance comparison with the previous tracking control are shown.