AbstractAtoms in most organic molecules are often carbon, oxygen, nitrogen, sulfur, halo- gens, etc. Based on the three-dimensional structure of a molecule, a molecular structural charac- terization (MSC) method called improved molecular electronegativity-distance vector (I-MEDV) was developed. It was used to describe the structures of 37 compounds ofstyrax japonicus sieb flowers. Through multiple linear regression (MLR), a QSRR model was built up. The correlation coefficient (R1) of the model was 0.980. Then, 4 vectors were selected to build another model through the method of stepwise multiple regression (SMR), and the correlation coefficient (R2) of the model was 0.975. Moreover, all the two models were evaluated by performing the cross-validation with the leave-one-out (LOO) procedure and the correlation coefficients (Rcv) were 0.948 and 0.968, respectively. The results show that the I-MEDV could successfully describe the structures of organic compounds. The stability and predictability of the models were good.