The structure-oriented lumping (SOL) method has been widely applied to molecular-level modeling and optimization in the refining industry. Calculating the physicochemical properties of products obtained by the SOL models can effectively guide the evaluation of product quality and optimization of the process. In this study, the SOL method was improved by extending the structural increments from 22 to 38 to describe the molecules in petroleum more accurately. According to the basic law that the properties and structures of molecules are inseparable, the structural increments with similar physical meanings were combined into a functional group to reduce the dimension to 11 characteristic parameters to describe the molecular structure, and a property prediction method that can be combined with the molecularlevel refining models based on the optimized SOL method was constructed. In addition, the accuracy of the selection and definition of the 11 functional groups was verified by analyzing and discussing the effects of functional groups on the properties, which, in turn, ensured the accuracy of the property prediction models. Compared with other property prediction methods, this method can be combined with the SOL method to provide reliable predictions of the boiling point, critical temperature, critical volume, critical pressure, density, cetane number, motor octane number, and research octane number of molecules.