Berberine is one of the most studied original natural drugs in China in recent years. It is a new lipid-lowering drug with completely different mechanism from statins, which has been used in the multi-center clinical trials. However, berberine is poorly absorbed in the intestinal tract after oral administration leading a significant pharmacokinetic characteristic of low blood concentration (1%) and bioavailability (< 5%). That is to say, it is difficult to explain the therapeutical effect in vivo by the current pharmacokinetic results. In fact, this phenomenon also exists in a number of clinically effective natural drugs. This review introduces the pharmacokinetic characteristic of berberine by focusing on the gut microbiota to mediate the metabolic process of berberine in vivo. Meanwhile, taking berberine as an example, we emphasized the important role of intestinal bacteria on the pharmacokinetic study on the oral chemical drugs, and put forward a new research mode of drug PK-PD mediated by the gut microbiota.