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A hypothesis for the three-dimensional structure of soil organic matter (SOM) and whole soil, based on an improved humic acid (HA) model that resulted from comprehensive investigations combining geochemical, colloid-chemical, electron-microscopic, IR, 13C-NMR, and X-ray spectroscopic as well as agricultural and ecological data with analytical pyrolysis, is proposed. Direct, temperature-programmed pyrolysis in the ion-source of the mass spectrometer combined with soft ionization in very high electric fields (Py-FIMS) and Curie-point pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) were the main thermal analytical methods employed. Molecular modeling and geometry optimization of SOM complexes and soil particles was performed using molecular mechanics and dynamics calculations in order to optimize the structural geometry and to determine low energy conformations. Atomic and molecular space requirements, voids, inter- and intramolecular hydrogen bonds, and water and metal cation interactions were evaluated. First investigations of quantitative structure-activity relationship (QSAR) properties were made to correlate molecular structures with soil properties such as mass, surface area, volume, partial charges (electronegativity), polarizability, refractivity, hydrophobicity, and hydration energy. Important characteristics of SOM such as surface activity, cation exchange capacity, binding and trapping of biological and anthropogenic substances, soil stabilization, and nutrient supply can be illustrated by these models.