OBJECTIVE Taking alkaloids and iridoid as the study, relationships of quantitative molecular structure and transmission rate on UF membrane were developed initially at exploring the mechanism of UF in Chinese herb decoction and to lay a foundation for the optimal design of membrane technology in the production of Chinese drugs preparation. METHOD The transmission rate of eight alkaloids and iridoid compounds in three UF membranes was determined, and quantitative structure-property relationships between quantitative molecular structure and transmission rate were developed by the data mining method of PLS or SVM. RESULT Quantitative structure-property relationship models of three membranes were developed by the data mining method of PLS or SVM, correlation coefficients were all greater than 0.9. The parameters in the models included LUMO, AlogP, CMR, K&H2, K&H3. CONCLUSION The relationship of UF transmission rate of these eight compounds and their molecular weight are not simply linearly dependent, the main factors which affect the UF transmission rate are capacity of gain or loss electron, hydrophilicity or hydrophobic and compound spatial structure.