Purple Grape Chalcedony from Indonesia has a special spherical appearance and violet color. Its double sides polishing waferis purple under the reflected light and brownish-yellow under the transmission light, while the color is concentrated in the center of the spherules. To investigate the origin of its color, a polarizing microscope, Scanning Electron Microscope, Microscopic UV-Vis Spectroscopy, heat treatment and LA-ICP-MS in situ composition analysis were performed. Chalcedony has a structure of fibrous core and micro quartz shell. The micro quartz shell has a particle size of 500 m, while the cryptocrystalline part is mainly composed of irregular SiO₂ particles with particle sizes less than 1 m. UV-Vis spectra show that the purple is mainly from the absorption of about 540 nm, while the yellow is due to the strong absorption of near-ultraviolet area and blue light generated by the “left-leaning” the spectrum. In the UV-Vis spectrum, the surface reflection error was corrected by the Selmeier equation, and the instrument error was subtracted from the intensity of the unabsorbed band. The intensity information of the 540nm absorption peak was obtained by deducting the baseline with the least square smoothing. Calculate the L^*a^*b^* and E^* values of chalcedony in purple tone under reflected light and yellow tone under transmitted light. Thus the color can be quantified. In the heat treatment experiment, the purple hue of chalcedony began to fade at about 350 ℃, and the absorption peaks of UV-Vis spectra at 390 and 540 nm disappeared, while the color difference between reflected and transmitted light decreased; both of them are yellow. As the temperature rises to 400 ℃, the brown tone deepens, and the peak of about 478 nm appears. The intensity of spectral increases during the heat treatment, the “left-leaning” intensification, and the peak “redshift”. This phenomenon is like the change of spectral of Fe /SiO₂ nanoparticles (Fe /SiO₂ NPs) during its growth.It may be related to the change of Fe-related fine structure or inclusions in chalcedony during heat treatment. Color parameter was combinate with in-situ composition analysis, the data were normalized by standard score (Z - score), compared the relationship of the value of E^* of purplecolor, the intensity of 540 nm peak and element content, found that 540 nm peak intensity can well reflect the concentration of purple. However, the linear correlation between color and the transition metal elements content is not significant. The E^* value of yellow tone has an approximately negative correlation with Fe content. Fe does not exist in the form of impurity minerals, and the color of chalcedony is not determined by the element content independently but is affected by Fe's existence in chalcedony, fine internal structure or inclusion.