Traditional Chinese medicine (TCM) and its natural products are complex mixtures containing hundreds of chemically different constituents but only a few components are responsible for the pharmacological effects and bioactivities. In order to clarify the functional mechanism of active compounds, the studies on metabolism are of great significance and necessity. Previously, research mainly focused on the aspect of pharmacokinetics, however in recent years, chemical metabolism of active compounds has drawn increasing attention. Researches on the chemical metabolism of single phytochemicals help to understand the transformation process in vivo and mechanism of action, also contribute to pharmacodynamics and toxicology studies and new drug development. In the present paper, the chemical metabolism of nine categories of phytochemicals was reviewed. This review focused on pharmacological action, metabolic characteristics, metabolic pathways, metabolites and assay method of alkaloids, flavonoids, saponins, terpenoids, stilbenes, phenols, quinones, lignans and esters. The parent drugs, perhaps the metabolites, or they together play a role in pharmacological effects. And different routes of administration may lead to different results of transformation pathways and metabolites. Moreover, high-tech assay methods, particularly the combined use of modern instrument analytical techniques, are beneficial to the research of drug metabolism.