The mesoporous carbon layers protected Fe-N nanocrystals (Fe-N-Csyn) was successfully synthesized by a simple hydrothermal approach and displays an improved oxygen bi-functional performance. The high specific surface area, mesoporous and graphitic carbon with more active sites of Fe-Nx and Fe3C/Fe in Fe-N-Csyn favors good synergistic electrocatalytic effect toward oxygen reduction and oxygen evolution reactions (ORR and OER) in alkaline medium. The bi-functional activity of Fe-N-Csyn was clearly observed from the earlier onset potential of 0.86 V and limiting current density of 5.23 mA cm−2 for ORR, as well as the low over potential of 470 mV with small Tafel slope value of 84 mV dec−1 for OER. The enhanced stability and improved oxygen bifunctional activity of Fe-N-Csyn catalyst was evidently demonstrated through an innovative synthesis approach for the development of earth-abundant metal catalysts for energy applications.