We study topological vortex phases in iron-based superconductors. Besides the previously known vortex end Majorana zero modes (MZMs) phase stemming from the existence of a three dimensional (3D) strong topological insulator state, we show that there is another topologically nontrivial phase as iron-based superconductors can be doped superconducting 3D weak topological insulators (WTIs). The vortex bound states in a superconducting 3D WTI exhibit two different types of quantum states, a robust nodal superconducting phase with pairs of bulk MZMs and a full-gap topologically nontrivial superconducting phase which has single vortex end MZM in a certain range of doping level. Moreover, we predict and summarize various topological phases in iron-based superconductors, and find that carrier doping and interlayer coupling can drive systems to have phase transitions between these different topological phases.
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