AbstractIn practical applications, when the mass of the hook cannot be ignored or the shape of the payload is irregular, the crane often exhibits the dynamic characteristics of double‐pendulum. Due to the complexity of double‐pendulum effect, the design of a controller for an three‐dimensional overhead crane with double‐pendulum effect is more complicated and more challenging. In addition, it is difficult to obtain satisfactory control performance due to the uncertainty of the parameters of the crane system. Moreover, the saturation constraint of the actuator is not considered, which may cause the actuator to saturate and severely degrade the control performance. Aiming at these practical problems, we propose a nonlinear controller based on energy analysis for the three‐dimensional overhead cranes system with double‐pendulum effect, while considering the saturation constraints of the actuator. Meanwhile, the asymptotic stability of the closed‐loop system is not only guaranteed. The comparative simulation and experimental results demonstrate the effectiveness of the proposed controller in trolley positioning and swing angles eliminating.