Bile salt vesicles (BSVs) are phases formed by the self-assembly of bile salts and phospholipids in the intestinal endogenous environment, which play a crucial role in the absorption of insoluble components. Reciprocal absorption of drug pairs is considered to be one of the potentiating mechanisms of herbal medicine compounding; however, the contribution of intestinal BSVs in the reciprocal absorption of drug pairs needs to be explored. In this study, Pueraria lobata-Salvia miltiorrhiza was used as a model drug pair. Puerarin (PUE), the main constituent of Pueraria lobata, and the predominant fat-soluble constituents of Tanshinone IIA (TSA) and Cryptotanshinone (CTS) and water-soluble constituents Danshensu (DSS) of Salvia miltiorrhiza were selected as model drugs. Blank BSVs, three co-loaded BSVs fabricated from Sodium Taurocholate and Egg Yolk Lecithin (TL/BSVs), and four mono-loaded TL/BSVs were subsequently prepared by the film hydration method. The co-loaded TL/BSVs prepared were BSVs for co-delivery of PUA and TSA (PT-TL/BSVs), BSVs for co-delivery of PUA and CTS (PC-TL/BSVs), BSVs for co-delivery of PUA and DSS (PD-TL/BSVs), prepared single drug-loaded TL/BSVs were BSVs for co-delivery of PUA and TSA (PT-TL/BSVs), BSVs for co-delivery of PUA and CTS (PC-TL/BSVs), BSVs for co-delivery of PUA and DSS (PD-TL/BSVs), and they were evaluated in vitro and in vivo. The effects of different drug-loaded TL/BSVs prepared in vitro and self-assembled TL/BSVs in the intestinal environment on the absorption of the "Pueraria lobata-Salvia miltiorrhiza" drug pairing were investigated by comparing the absorption of three combinations of PUA-TSA, PUA-CTS, and PUA-DSS in the bile and bile-less models. The endogenous BSVs were approved to have positive effect on the intestinal absorption of the "Pueraria lobata-Salvia miltiorrhiza" medicine pair, due to their solubilization effect on PUA, TSA, CTS, DSS. Moreover, compared with mono-loaded BSVs, the better structural stability of co-loaded BSVs was observed, which is beneficial to the BSVs'intestinal transportation and the absorption of the active compounds of Pueraria lobata-Salvia miltiorrhiza. Accordingly, this work demonstrates that the BSVs plays an important role in the reciprocal absorption of drug pairs, which provides a new research perspective for elucidating the modern scientific connotation of drug pair compatibility.