Gantry cranes, which have attracted extensive attention, are mostly simplified as nonlinear single pendulum systems without load hoisting/lowering. However, in fact, due to the existence of the hook, gantry cranes produce double pendulum swing. With an extra underactuated degree of freedom, the anti-swing control of the double pendulum gantry cranes becomes more difficult than that of single pendulum gantry cranes, especially when load hoisting/lowering is considered simultaneously. Moreover, large swings, which lead to problems such as inaccurate positioning and low transportation efficiency, may be caused by double pendulum gantry cranes with load hoisting/lowering. In this paper, a nonlinear coupled tracking anti-swing controller is proposed to solve these problems. In this controller, a smooth tracking trajectory is introduced to ensure the stable start and run of the trolley, and a coupled signal is constructed to eliminate the residual swing angles of gantry crane system. The system stability is analyzed by using Lyapunov method and Barbarat theorem. Theoretical derivation, simulation and experimental results show that the proposed controller has excellent control performance, specifically, not only does it ensure accurate positioning of the load, but also it suppresses and eliminates the hook/load swing angle effectively. The proposed controller can still achieve good control effects and has strong robustness under the condition of changing the load mass, trolley target displacement, system initial swing angles and adding external disturbance.