Abstract: Based on the molecular topology,distance matrix is used to describe molecular structure and different factors are used to distinguish the difference among the atoms in molecules,a new method is developed which can be used to study the structure-property re lationship of molecules containing heteroatoms.The method is used to study the relationship between the density and molecular structure of mercaptan and thioether,and a quantitative relation is proposed that it can be used to characterize the structure-property relationship and to predict the density,The results calculated show that the predicted densities are in good a greement with the experimental data,and the mean relative deviation is 0.313%.Not only the quantitative relation developed in this paper can predict the densities of mercaptan and thioether,but can help to understand the structure-property relationship.