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In order to reveal the chemical substance basis of pharmacodynamic effects of Zuotai, energy dispersive spectrometry of X-ray (EDX), X-ray fluorescence spectroscopy (XRF), synchrotron radiation X-ray absorption fine structure (SR-XAFS), X-ray diffraction (XRD), scanning electron microscope (SEM) and atomic force microscope (AFM) were used to analyze the elements, the chemical valence and local structure of mercury, and the chemical phase composition and micro-morphology of Zuotai. EDX and XRF analysis shows that the main elements in Zuotai are Hg and S, with some other minor elements, such as 0, Fe, Al, Cu, K, Ag, Ca, Mg etc. SR-XAFS analysis shows that: the oxidation state of mercury in Zuotai is divalence, its neighbor atoms are S, and its coordination number is four. XRD assay found that β-HgS (cubic, F-43m 216) and S8 (orthorhombic, Fddd 70) are the main phase compositions in Zuotai. Besides, it also has a small amount of C (hexagonal, P63/mmc 194), Fel.05 S0.95 (hexagonal, P63/mmc 194), Cu6S6 (hexagonal, P63/mmc 194), Cu1.8 S (cubic, F-43m 216) and so on. And it was found that the crystallinity of Zuotai is about 59%, and the amorphous morphology substance in it is about 41%. SEM and AFM detection suggests that Zuotai is a kind of ancient micro-nano drug, and its particle size is mainly in the range of 100-600 nm, even less than 100 nm, which commonly further aggregate into several to 30 µm loose amorphous particles. In summary, the present study elucidated physicochemical characterization(elements composition, coordination information of mercury, phase composition and micro-morphology) of Zuotai, and it will play a positive role in promoting the interpretation of this mysterious drug.