The realization of Majorana zero modes in condensed matter have been attracting enormous interests from fundamental science such as topological quantum computation. Recently iron based superconductors were identified as a high-temperature platform for realizing topological superconductivity and Majorana modes. As unconventional superconductors, one of the most important characteristics of them is that they are in the vicinity of magnetic states due to the strong Hund’s coupling in iron atoms. Here we propose that the line defects with missing Te/Se anions in Fe(Se, Te) superconductors provide the realization of intrinsic antiferromagnetic (AFM) chains with Rashba spin-orbit coupling. Against conventional wisdom, Majorana zero modes (MZMs) can be robustly generated at these AFM chain ends. These results can consistently explain the recent experimental observation of zero-energy end states in line defects of monolayer Fe(Te, Se)/SrTiO3 by scanning tunneling microscopy (STM) measurements. Our research not only demonstrates an unprecedented interplay among native line defect, emergent magnetism and topological superconductivity but also explores a high-temperature platform for Majorana fermions.