Coptis chinensis Franch. is one of the most important medicinal plants globally. However, this species contains relatively high concentrations of chromium (Cr) which potentially detrimental to human health. It is important to understand Cr localization and speciation in order to evaluate its accumulation and transportation mechanisms and minimize Cr transfer to humans. As little previous work in this area has been carried out, we utilized synchrotron radiation microscopic X-ray fluorescence (SR-μXRF) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) to spatially locate Cr, X-ray absorption near-edge spectroscopy (XANES) to analyze Cr speciation, and inductively coupled plasma mass spectrometry (ICP-MS) to detect Cr subcellular concentration. Micromapping results showed that Cr was distributed predominantly within the vascular cylinder, the periderm and some outer cortex, and the cortex and some vascular bundles in root, rhizome, and petiole, respectively. XANES data showed that Cr(VI) can be reduced to Cr(III) when grown with Cr(VI), and yielded a novel conclusion that this plant contain elemental chromium. ICP-MS data showed that Cr was primarily compartmentalized in cell walls in all tissues. The new insights on Cr accumulation in C. chinensis Franch. provide a theoretical basis for the evaluation of Cr in other medicinal plants.