Metabolisms of herbal remedies and their natural components, which play a critical role in support of medicine development, and clinical medication, are drastically different from those of designed drugs. The separation, isolation and identification of drug metabolites from complex endogenous matrices like urine, plasma and tissue extracts are extremely challenging. For herbal medicine studies, it is even more difficult due to the complex chemical composition. Usually, a combination of high performance liquid chromatography (HPLC) and mass spectrometry (MS) is proven to be a powerful analytical tool for screening and identifying drug metabolites. For suitable instruments, the quadrupole time-of-flight (Q-TOF), hybrid ion trap time-of-flight (IT-TOF), and orbitrap mass spectrometry could clearly enhance the efficiency in metabolite profiling compared to general triquadrupole (QQQ) and ion trap (IT) mass spectrometry technique. Due to the ability for unambiguous structure determination, nuclear magnetic resonance spectroscopy (NMR) is also coupled to HPLC for on-line analysis of metabolites. Capillary electrophoresis and gas chromatography are also optional methods. These techniques could provide abundant information from a wide variety of samples. However, in many cases, preparations of metabolites are critical for further pharmacokinetics, pharmacologic, and toxic evaluation of the remedy. Therefore, accumulations of metabolites from the in vivo biological samples are essential. Biotransformation models are considered to be important complementary sources for preparation of drug metabolites. Fungi, plant cells, and a variety of enzymes were used to provide information for further in vivo testing. This review focuses on the screening and identification of drug metabolites of herbal medicines.