The near edge X-ray absorption fine structure (NEXAFS) spectra of naphthalene diimide molecules with increasing degrees of thionation show distinct and systematic changes in the C 1s → π ∗ manifold. However, interpretation of such spectra is difficult using experimental data alone, due to the limitation in experimental NEXAFS resolution. In this work, we have calculated the NEXAFS spectra of naphthalene diimide molecules with increasing degrees of thionation using the density functional theory-based eXcited electron and Core Hole approach. We find that the systematic broadening and intensity reduction in the peaks observed in the π ∗ manifold with increasing thionation are the result of distinct changes in the chemical environment of the outer carbon atoms that are bonded directly to either oxygen or sulfur. Specifically, the C 1s → lowest unoccupied molecular orbital (LUMO) transition energy dramatically decreases with thionation, as the valence electron density of these carbon atoms is increased when highly electronegative oxygen atoms are replaced by less-oxidizing sulfur atoms. It is also shown that significant core level shifts present in naphthalene diimide-based molecule result in a mixing of the LUMO and LUMO + 1 character in the C 1s → π ∗ manifold, meaning that experimentally observed peaks cannot be uniquely associated with the transitions of LUMO, LUMO + 1, etc.