A novel methodology to characterize gasoline and diesel streams into the molecular level is developed on the basis of molecular type homologous series (MTHS) matrix framework (Chem Eng Sci 2005, 60, 6702-6717) The method comprises the enhancements of both representation matrix construction and transformation methodology of bulk properties Into molecular composition To Improve the accuracy and adequacy of the representation model, different strategies are set up separately for gasoline and diesel streams for the consideration of isomers By introducing statistical distribution and applying extensive bulk properties, the transformation approach is revolutionized to increase the usability, and tackle the challenge of possibly achieving significantly different molecular compositions from the same bulk properties of refining streams by existing transformation approaches The proposed method is verified with both gasoline and diesel streams, and the results show a good agreement with measured data