The pharmacokinetics of Chinese materia medica (PCMM) has made a great contribution to investigations of the in vivo process of various components in Chinese materia medica (CMM), intending to provide useful information for clinical guidance related to CMM. However, some issues are worthy of further consideration, and current PCMM studies face a substantial challenge. First, high-dosage administration is prevalent in PCMM studies, and the obtained results might be meaningless and inappropriate for guiding the clinical application of CMM, as they deviate from clinical practice. Improvements in instrument sensitivity have not reduced the prevalence of high-dosage administration. In addition, the selection of components for detection in PCMM studies is usually uncertain, lacking sufficient scientific support, especially for components without clarified bioactivities. Therefore, the scientific value of current PCMM studies is limited. We believe that these abnormalities can be attributed to the poor recognition of the characteristics of CMM and the improper application of research approaches from Western medicines. Currently, the more pressing key scientific issues for CMM should be clinical effectiveness, quality control and bioactivity discovery, which are closely related to its own characteristics and are beneficial to its modern developments.