Advanced technologies are used to clarify the meridian tropism theory of traditional Chinese medicine is an important part of theoretical studies of traditional Chinese medicine. In this article, modern pharmacokinetic method was used to investigate tissue distribution characteristics of psoralen and isopsoralen of Psoraleae Fructus decoction in rats, in order to provide research ideas and experimental basis for the meridian tropism theory. In this study, various tissue samples such as heart, liver, spleen, lung, kidney, brain and spermary were collected at different times after oral administration with FP decoction, in order to determine concentration of psoralen and isopsoralen by HPLC. Pharmacokinetic parameters were calculated by DAS 2.0 software. The study results showed that HPLC indexes of psoralen and isopsoralen in various tissues of rats met the determination requirements of biological samples. Both components were distributed in all of the tissues, with AUC(0-t) order of liver > lung approximately kidney > heart > brain approximately spleen > spermary. There was significant difference between liver, kidney, lung and other tissues (P < 0.05). MRT(0-t) of both psoralen and isopsoralen were about 10 h. Therefore, psoralen and isopsoralen showed stronger targeting selection in liver, kidney and lung.