Hexagonal manganites REMnO3 (RE, rare earths) have attracted significant attention due to their potential applications as multiferroic materials and the intriguing physics associated with the topological defects. The two-dimensional (2D) and 3D domain and vortex structure evolution of REMnO3 is predicted using the phase-field method based on a thermodynamic potential constructed from first-principles calculations. In 3D spaces, vortex lines show three types of topological changes, i.e. shrinking, coalescence, and splitting, with the latter two caused by the interaction and exchange of vortex loops. Compared to the coarsening rate of the isotropic XY model, the six-fold degeneracy gives rise to negligible differences with the vortex-antivortex annihilation controlling the scaling dynamics, whereas the anisotropy of interfacial energy results in a deviation. The temporal evolution of domain and vortex structures serves as a platform to fully explore the mesoscale mechanisms for the 0-D and 1-D topological defects.