The calculation of chemical structures and physical properties is the basis of petroleum refining optimization. In this article, a method to build an average molecule model for hydrocarbons and petroleum fractions is developed. 1 H-NMR, molecular weight, and elemental composition were used as input parameters to construct a single molecular model that represents the average chemical structure. The average molecules were constructed by assembling the average building blocks, which are a set of predefined structural fragments, covering typical hydrocarbon and heteroatom functional groups in petroleum systems. After applying a group contribution method to the derived molecule, the bulk property of a sample could be directly calculated. The method was validated by being applied to various model compounds (including paraffins, cycloalkanes, aromatics, and heteroatom-containing species), where it successfully predicted the average building blocks, unit sheets number, and physical properties. The application of this method to petroleum fractions was demonstrated.