Abstract: Using ultra high performance liquid chromatography (UHPLC) coupled with mass spectrum (MS) technology, a method has been established for separation and analysis of alkaloid isomers. Alkaloids in Ephedra sinica transitionally crossed blood brain barrier (BBB) and the distribution were investigated. The concentrations of Ephedra alkaloids in rat central nervous system (CNS) were determined to acquire the distribution characteristics and differences in cerebral cortex, cerebellum, hippocampus, striatum, medulla oblongata and hypothalamus. It was founded that pseudoephedrine, norephedrine, norpseudoephedrine, methylephedrine (methylpseudoephedrine) were able to cross BBB fast via gastro-intestinal tract after administrated with Ephedra sinica. Cortex and hippocampus was the main distribution region, followed by hypothalamus, striatum and cerebellum, in which medulla oblongata had the least. The distribution of various alkaloids, as AUC_{0-t, brain}/AUC_{0-t, blood} was ephedrine > methylephedrine > demethyl ephedrine. Alkaloids in Ephedra sinica crossed BBB rapidly, showing the regional distribution tendency in central nervous system, and the distribution was diversity. This group of data provides distribution of bioactive constituents of Ephedra in CNS.