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The holistic system of traditional Chinese medicine (TCM) is reflected by the integrity of the ingredients contained in herbal medicines, which creates a challenge in establishing quality control standards for raw materials and the standardization of finished herbal drugs because no single component contributes to the total efficacy. Thus, the chromatographic fingerprinting technique of TCM has proved to be a comprehensive strategy for assessing the intact quality of herbal medicine, since the origin of the herbal medicines could be identified and classified based on so-called phytoequivalence. On the other hand, chromatographic fingerprinting is essentially a high-throughput technique and an integral tool to explore the complexity of herbal medicines. In order to further control the comprehensive quality of TCMs, some strategies are proposed to trace the chemical changes of chromatographic fingerprints both in product processing and/or after their administration by modern chromatographic techniques and chemometrics. Combined with the techniques developed in systems biology, it seems also possible to reveal the working mechanism of TCMs and to further control their intrinsic quality.