A work efficiency and safety of Mobile Harbor crane in the open sea condition are considered as serious problem because Mobile Harbor have 6 degree of freedom motion caused by external disturbance such as wave and wind. It is the core technology to suppress the sway and surge motion of containers during loading and unloading operation in this Mobile Harbor project. KAIST Mobile Harbor center proposed and implemented the dual stage control system to resolve this problem. In this paper, we proposed the anti-swing controller using this dual stage control system. To establish the system model, system parameters are characterized by system identification process with respect to the 1/20 scale D4 crane model and the LQR controller for anti-swing was designed based on decoupled of X- and Y-axis and linearized crane model. The performance of the designed anti-swing LQR controller is verified by experiments of 1/20 scale Mobile Harbor crane mounted on a shaky motion platform even though the mode of motion of container was excited.