Electrospray ionization mass spectrometry (ESI-MS) is becoming an important tool in the study of natural organic matter (NOM) at the molecular level. Ultrahigh-resolution ESI-MS analyses of NOM often produce very complicated spectra; therefore, visual presentation and structural interpretations of the spectra are difficult. To meet this analytical challenge, we herein propose and demonstrate an approach using the van Krevelen diagram. With this approach, complicated mass spectra can be visualized in a way that allows for (1) possible reaction pathways to be identified and presented, and (2) qualitative analyses on major classes of compounds that comprise ultrahigh-resolution spectra. The qualitative analyses are in a good agreement with results obtained from analyses by other analytical techniques. Additionally, the van Krevelen diagram can be expanded to a 3D plot by using peak intensities or relative intensities as the z-axis. The 3D van Krevelen diagram allows for an evaluation of the relative significance of structurally related compounds. The 3D plot can also be a useful tool for compositional differentiation among samples.