In this research, micro Coix lacryma-jobi L. vertical flow constructed wetlands (VFCWs) were set up using domestic sewage (DWS) and 1/2 Hoagland nutrient solution (HNS) as VFCWs water sources. 0, 20 mg L−1 and 40 mg L−1 of Cr6+ (in the form of K2Cr7O2) were added into the water sources separately in order to study the response of Coix lacryma-jobi L. under Cr6+ stress. The results showed that the inhibition rates of Cr6 + on plant height, stem diameter, shoot and root dry weight treated with HNS were 2.88~10.16%, 5.12~11.86%, 3.53~6.51% and 2.89~6.34% higher than those in DWS treatment. SEM analysis showed that the nuclear bilayer membrane was slightly damaged, the chromatin decreased and the number of mitochondrial cristae decreased when treated with 20 mg L−1 of Cr6+, however, organelle damage was more severe under 40 mg L−1 of Cr6+exposure. The X-ray energy spectrum analysis results indicated that the accumulation of chromium in epidermis and endodermis were higher than those in stele. The contents of total Cr in roots, stems and leaves treated with HNS were higher than those of DWS treatment. The highest content of Cr was observed in cell wall (32.12–188.1 mg kg-1), followed by vacuole (5.0–38.14 mg kg-1). The contents of Cr in each subcellular component in roots, stems, and leaves treated with HNS were higher than those of DWS, except for organelle components in the 14th week. DWS was used as water influent, the contents of easily migrated combined Cr (ETM) in roots, stems and leaves were significantly lower than those in HNS treatment. Improving the nutritional conditions of constructed wetlands might be beneficial to the improvement of their ability to purify chrome-containing waste water.