Herbal medicine is an inseparable part of the traditional medical science in many countries, especially Eastern ones, throughout the history. Nowadays, the popularity of using herbal medicines in daily life, as well as clinical practice, has gradually expanded to many Western countries with positive impacts and acceptance. The annual growth of the herbal medicine and natural product market has strongly inspired scientists to standardize and formulate herbal sources via present pharmaceutical criteria as modernization of traditional medicines. Based on the shared knowledge of traditional medicines using herbs, scientists take advantage of modern sciences (chemistry, biology, etc.) and powerful computing advances to develop many types of herbal metabolite databases with various focuses, such as network pharmacology and virtual screening. The recent rise of these databases has intensively supported modern drug discovery of the natural molecular framework. Although the number of known natural compounds sourced from plants, bacteria, and fungi, especially compounds evaluated for bioactivities is very small compared to the synthetic organic counterpart, the essential role of natural compounds in general and herbal metabolite, in particular, is undeniable with the fact that over 50% of approved drugs have herbal origins and millions of them have been experimentally validated for bioactivities. Currently, the herbal metabolite databases are diverse in capacities, focuses, and locality so that scientists, as well as non-expert users, have a broad range of choice for study purposes. In this work, we critically reviewed 30 herbal metabolites databases and performed comparative analysis among 18 accessible non-commercial ones as a guideline of data source for modern drug discovery.