This study investigated the protonation of nitrogen atoms in porphyrins with meso-phenyl p-substituted by an electron-withdrawing group using N 1s X-ray photoelectron spectroscopy (XPS), the N K X-ray absorption near-edge structure (XANES), and the discrete variational (DV)-Xalpha molecular orbital (MO) method. Both tetraphenylporphyrin (TPP) and tetrakis(p-sulfonatophenyl)porphyrin (TSPP) have a single structure: the former has two protonated and two non-protonated N atoms in the porphine ring; the latter has four protonated N atoms in the porphine ring. In contrast, a combination of XPS, XANES, and DV-Xalpha MO calculations shows that tetrakis(p-carboxyphenyl)porphyrin (TCPP) has a dual structure: one structure has two protonated and two non-protonated N atoms; the other has four protonated N atoms. Furthermore, this result was also considered based on the protonation constants of N atoms in the porphyrins. The correlation between the strength of electron-withdrawing groups and protonation to N atoms in porphyrins can be described using the spectral patterns of the N 1s XPS and N K XANES spectra.