A scheme is proposed for the fast generation of three-dimensional entanglement between two atoms trapped in two cavities connected by a fiber via invariant-based shortcut to adiabatic passage. With the help of quantum Zeno dynamics, the technique of invariant-based shortcut is applied for the generation of two-atom threedimensional entanglement. The numerical simulation results show that the target state can be generated in a short time with a high fidelity and the scheme is robust against the decoherence caused by the atomic spontaneous emission, photon leakage, and the variations in the parameters. Moreover, the scheme may be possible to be implemented with the current experimental technology.