Natural products are the most representative form of conventional therapy as compared to any other traditional or alternative medicine systems. They have numerous active components, either primary or secondary metabolites, which are associated with the diverse, intricate, and distinct characteristics of natural products and result in various pharmacological effects in clinic. However, some problems are associated with research on herb quality, which is the core of the drug industry, and restrict the development of this field to a certain extent. Quality-markers (Q-markers), a novel concept for quality assessment, open up a new avenue for promotion of healthy development of traditional medicine industry and improvement of the quality standard system to enhance traditional medicine or product quality standards. In this study, we first summarized the main factors affecting the quality of traditional medicines and natural products and importance for safety and then presented the concept of background and relevant factors of Q-markers. Moreover, the modern science technology and related methods used to identify the chemical composition have been discussed. Especially, based on the systematic analysis and discussion of the basic properties and clinical features of natural products, we have discussed new trends and effective strategies for identifying relevant Q-markers from herbs and probed the future research directions and challenges.