We demonstrate how the near-edge X-ray absorption fine structure (NEXAFS) spectroscopy of single and double core-hole states created by the ionization of a heteroatom can be used to probe subtle changes in intramolecular chemical environments that are nearly indistinguishable by conventional NEXAFS spectroscopy. Using prototypical organic molecules (2/3-pentanone and pentanal), we show how new spectral features emerge in the C K-edge NEXAFS spectra, when creating single and double core-holes at the oxygen heteroatom site. The effect on the lowest unoccupied molecular orbitals is analyzed by studying the double-core-hole-induced ultrafast valence electron dynamics of the three molecules. The predicted changes from our simulations should be observable with state-of-the-art experiments at X-ray free-electron lasers.