Color is one of the most important factors in evaluating the quality and price of jewelry. Quantitative research on color of jewels has been a hotspot in gemological science. Whether for jewelry industry or gems research, observing and describing the gems’ color characteristics under transmission light is an essential method. This study focuses on building a research method to quantitatively characterize nephrite color, and to determine their color origin based on transmitted spectroscopy techniques. Natural gray-purple nephrite of Sanchahe mining, Qinghai, China was chosen as a typical subject due to its gradual-change color characteristic. We first quantitatively expressed and replicated the different color region on a gray-purple nephrite sample with given thickness (1.0 mm) with UV-Visible absorption spectra and 1976 CIE L*a*b* colorimetric parameters, as well as Adobe Photoshop software. The replicated color of light and dark color regions were both close to the transmitted color observed by naked eyes. It is inferred that the subtle color differences between naked eyes observation and transmitted spectroscopy replication may from the multiple effects of incident light in translucent polycrystalline structure, such as absorption, refraction, diffraction, scattering, and so on. As for the purple color origin, Laser Ablation Inductively Coupled Plasma Mass Spectroscopy (LA-ICP-MS) showed an increase of the concentrations of manganese (Mn) as the nephrite color becomes darker. Moreover, the emission peak at 585 nm on Photoluminescence (PL) and absorption peak at 530 nm on Ultraviolet Visible (UV-Vis), and the sextet Mn2+ resonance peaks on Electronic Paramagnetic Resonance (EPR) provide solid support to prove that Mn2+ should be the main factor contributing to the purple color. This work provides a specific experimental method on quantitative observing and describing the color of gems under transmitted light, and it also offers valuable information on determining the chromophores and color origin.