Accompanying with hot discussions on developing multi-target drugs for the therapy of multi-gene diseases, herbal medicines are receiving more and more attention worldwide in both academic and industrial fields. Pharmacokinetic and metabolic research is one of the important issues for intensive understanding of therapeutic benefits/risks of herbal medicines. The qualitative and quantitative analysis of herbal medicines, which is a prerequisite for pharmacokinetic and metabolic evaluations, remains a great challenge because of the intrinsic complexity of herbal medicines. This paper provides a review on the recent development of qualitative and quantitative methodologies on herbal medicines analysis. Powerful hybrid mass spectrometric tools such as Q-TOF and IT-TOF are highly useful for both the qualitative and quantitative analysis of complicated components. In the past decade, some universal useful strategies to the qualitative and quantitative analysis and pharmacokinetic assessment of complicated herbal components have been also proposed. Nonetheless, it is urgent to develop additional strategies to resolve the critical challenges underlying herbal analyses, such as the lack of authentic compounds, the difficulties in information processing, and the elimination of complex matrixes interferences.