Panax notoginseng is used as a therapeutic agent in Chinese medicine for stopping hemorrhage and also as a general health remedy. Although Panax notoginseng saponins (PNS) are currently attracting attention due to their hemorheological properties, the absorption profiles of PNS have still not been fully investigated. In the present study, an in situ intestinal perfusion rat model was used to investigate the absorption mechanism of sanchinoside R1 (R1) and ginsenoside Rg1 (Rg1), two main components of PNS. Quantitative analysis methods for R1 and Rg1 were first established, then concentrations of R1 and Rg1 in the perfusate were measured in real time through assessment of circulating perfusate in the rat small intestine. The absorption rate constant (k(a)) values for R1 were 0.1223, 0.0946 and 0.0904 h(-1) at a dose of 1, 10 and 100 mg respectively, while those of Rg1 were 0.1169, 0.1134 and 0.1089 h(-1) at a dose of 1, 10 and 100 mg respectively. The optimal absorption site for both of these compounds was found to be the duodenum, which indicated that the bioavailability of the orally administered PNS preparation was relatively low. Finally, the effect of certain absorption promoters on the absorption rates of R1 and Rg1 was investigated. It was found that carbomer and borneol could enhance the permeability of R1 and Rg1 on the intestinal wall (P < 0.05), which indicated that a suitable absorption promoter could improve the absorption of PNS and increase its bioavailability.