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We investigated the effects of long-time thermal oxidation (LTO) of nitrogen-doped multiwalled carbon nanotubes (N-MWCNTs) at 330 °C in air. By scanning electron microscopy (SEM), high-resolution transmission electron microscopy (TEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), thermogravimetric analysis, Raman spectroscopy and cyclic voltammetry we characterize the oxidized N-MWCNTs (Ox-NMWCNTs). SEM and TEM characterizations revealed that LTO promoted structural damages driven by Fe-based nanoparticles, producing holey N-MWCNTs. The XRD patterns showed that short times of oxidation process, encapsulated Fe3C, and α-Fe nanoparticles in N-MWCNTs cut or perforate their graphite layers. For LTO (>300 h), Fe3C and α-Fe nanoparticles are transformed into Fe3O2 (hematite structure). Deconvolution analysis of the (0 0 2) crystallographic planes allows us to monitor the graphitization evolution of the Ox-NMWCNTs. XPS characterization demonstrated that the surface composition of Ox-N-MWCNTs is influenced by the LTO, while carbon and nitrogen decrease in percentage, the oxygen increases. We have found that LTO favored the formation of pyrrolic nitrogen doping. The holey N-MWCNTs are a porous material with a moderate surface area. According to the voltammetry studies, when the Ox-N-MWCNTs are acid-treated, the surface area is doubled and presents a double layer capacitance that could be advantageous for energy applications.