Nitrogenated holey graphene (NHG) has attracted much attention because of its semiconducting properties. However, the stacking orders and defect properties have not been investigated. In this letter, the structural and stacking properties of NHG are first investigated. We obtain the most stable stacking structure. Then, the band structures for bulk and multilayer NHG are studied. Impact of the strain on the band gaps and bond characteristics is discuss. In addition, we investigate formation mechanism of native defects of carbon vacancy (V C ), carbon interstitial (C i ), nitrogen vacancy (V N ), and nitrogen interstitial (N i ) in bulk NHG. Formation energies and transition levels of these native defects are assessed.