Designing　atomic　defects　engineering　is　significant　for　boosting　the　activity　of　metal　catalytic　sites.　Herein,　we　constructed　Fe-N4　sites　on　defective　N-doped　carbon　catalyst　(Fe-N4/def-CN)　by　in-situ　ZnO　thermal　etching　strategy.　Compared　with　defect-free　Fe-N4/CN,　Fe-N4/def-CN　had　a　half-wave　potential　(E1/2)　of　0.920　V　vs　RHE　for　alkaline　ORR　with　50　mV　increasing.　We　directly　observed　the　ZnO　in-situ　disappearance,　studied　ZnO　thermal　etching　effect　on　CN　substrate　and　revealed　the　mechanism　of　carbon　defect　formation　by　in-situ　envi-ronmental　transmission　electron　microscopy　(ETEM)　and　in-situ　X-ray　diffraction　(XRD)　measurements.　Density　functional　theory　(DFT)　calculations　demonstrated　the　easier　formation　of　double　carbon-atoms　defects　adjacent　to　Fe-N4　sites.　The　carbon-atoms　defects　and　Zn-atom　vacancies　synergistically　improved　the　ORR　activity　of　Fe　-N4　sites.　This　work　provides　a　atomic-level　insight　to　optimize　the　atomic　defects　engineering　of　metal-N4　sites,　such　as　carbon-atoms　defects　and　metal-atoms　vacancies　by　in-situ　ZnO　thermal　etching　strategy.