The Chinese drug pair Danshen (Salvia miltiorrhiza)-Sanqi (Panax ginseng) has been widely used for centuries treating various cardiovascular disorders, among which salvianlic acid B (SAB), ginsenoside Rg(1) (GRg(1)), ginsenoside Rb-1 (GRb(1)) and notoginsenoside R-1 (NGR(1)) were identified as the major components. The present study focused on the interaction between these components based on investigating their intestinal absorption using the Ussing chamber technique. The concentrations of SAB, GRg(1), GRb1 and NGR(1) in the intestinal perfusate were determined by LC-MS/MS method, followed by Q (accumulative quantity) and P-app (apparent permeability). The results showed that all these four main components displayed very low permeabilities, which implied their poor absorption in the rat intestine. The intestinal absorption level of SAB displayed regioselectivity: duodenum < jejunum < ileum. However, there was no significant difference in the absorption of GRg(1) and GRb(1) in the different segments. The Q and P-app values of the four main components were obviously increased in jejunum when co-administrating Danshen extract with Sanqi extract. In conclusion, compatibility of Danshen and Sanqi could remarkably improve the intestinal absorption level of the main components in the pair. To some extent, this might explain the nature of the compatibility mechanisms of composite formulae in TCMs.