An enhanced coupling nonlinear tracking control method for an underactuated 3D overhead crane systems is set forth in the present paper. The proposed tracking controller guarantees a smooth start for the trolley and solves the problem of the payload swing angle amplitude increasing as the transferring distance gets longer for the regulation control methods. Different from existing tracking control methods, the presented control approach has an improved transient performance. More specifically, by taking the operation experience, mathematical analysis of the overhead crane system, physical constraints, and operational efficiency into consideration, we first select two desired trajectories for the trolley. Then, a new storage function is constructed by the introduction of two new composite signals, which increases the coupling behaviour between the trolley movement and payload swing. Next, a novel tracking control strategy is designed according to the derivation form of the aforementioned storage function. Lyapunov techniques and Barbalat's Lemma are used to demonstrate the stability of the closed‐loop system without any approximation manipulations to the original nonlinear dynamics. Finally, some simulation and experiments are used to demonstrate the superior transient performance and strong robustness with respect to different cable lengths, payload masses, destinations, and external disturbances of the enhanced coupling nonlinear tracking control scheme.