Abstract: The "toxicity" and safety of traditional Chinese medicines have been seriously concerned. Alkaloids are the main pharmacodynamic components of many kinds of traditional Chinese medicines, which show strong biological activity at low concentration. It will also cause toxic side effects but if used improperly. Some alkaloids are both active and toxic, and the safety of related traditional Chinese medicines is particularly noteworthy. The efficacy or toxicity of alkaloids may be the result of the combined action of parent compounds and metabolites, which is not only related to the structural types of compounds, but also has obvious species differences between humans and animals. This review focused on the alkaloids contained in the "toxic" traditional Chinese medicines that are officially recorded in Chinese Pharmacopoeia and the metabolism patterns of alkaloids with different structures as well as the enzymes involved were summarized and discussed by referencing the publications in recent two decades. The present study will be beneficial to the rational use of these traditional Chinese medicines in clinic.