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Agate attracts the attention of gem mineralogists because of its variable colors. The color of agate is closely related to its naming and classification, so it is necessary to study the color and mineral origin of agate. In this paper, the mineralogical characteristics and color origin of red, yellow and green Moqi agates from Inner Mongolia were systematically studied by means of Fourier transform infrared spectrometer, Raman spectrometer, X-ray powder diffractometer, electron probe microanalyzer and ultraviolet–visible spectrophotometer. It is found that the color of Moqi agate is related to the minerals and trace elements contained in it, and is associated with the electron transition or charge transfer of Fe ions in the contained minerals. Green agate has the highest Fe content, and its color is caused by celadonite inclusions. The red and yellow color in Moqi agate is mainly caused by hematite and goethite, while red agate contains more Fe than yellow agate. Raman spectroscopy and X-ray diffraction analysis show that the content of moganite in Moqi agate is 0–30%. It is calculated that the crystallinity of Moqi agate is 1.5–3.5. This work provides a theoretical basis for future research on the identification of Moqi agate. [ABSTRACT FROM AUTHOR]