At present, marine resources, especially the deep-sea resources, are becoming more and more important in resource exploitation globally, and hence, widely used deep-sea cranes are playing essential roles. For such systems, the bridge frames and trolleys are set up above the water, while payloads are transported under the water. In this underwater situation, there exist hydrodynamic forces such as complicated disturbances to the crane systems, making the payload vibration and rope flexibility more obvious. For the sake of improving working efficiency, considering the constraints of all the state variables, an anti-vibration trajectory is designed for the trolley motion, which can not only ensure trolley positioning but also suppress the flexible payload’s vibrations. Then, the state variables are constrained within preset safety ranges. Finally, numerical simulation results prove the satisfactory performance of the designed method.