The purpose of the present study was to study the mechanisms of salvianolic acid B phospholipid complex loaded nanoparticles (SalB-PLC-NPs) enhancing the oral bioavailability of SalB by in situ perfusion model in rats and to evaluate the potential of phospholipid complex loaded nanoparticles (PLC-NPs) serving as an efficient oral delivery system to enhance the bioavailability of highly water-soluble drugs. SalB-PLC-NPs, prepared by a solvent evaporation method, exhibited a spherical shape with a mean particle size and a zeta potential of 112.2 nm and -44.2 mV, respectively. The drug entrapment efficiency and drug loading were 86.19% and 3.21%, respectively. The lyophilized SalB-PLC-NPs, prepared with 10% maltose as the cryoprotectant, presented sustained release profiles in artificial gastric juice (0.1 M HCl with pH 1.2) and intestinal juice (PBS with pH 6.8 and 7.4). The absorption mechanisms were studied using a modified in situ perfusion method in rats, which showed the segment dependent absorption characteristics of SalB, SalB-PLC as well as SalB-PLC-NPs. The greatest absorption was obtained when SalB-PLC-NPs were perfused in colon. The possibility of intestinal lymphatic transport of SalB-PLC-NPs was investigated using mesenteric lymph vessel cannulation. Microscope (fluorescence and natural light) observation of lymph indicated that nanoparticles underwent intestinal lymphatic transport. In conclusion, the enhanced oral bioavailability of SalB was contributed to both the PLC and NPs. Importantly, our studies indicate that PLC-NPs may be a promising delivery system to enhance the oral bioavailability of highly water-soluble drugs.