The physiological mechanisms and phytoremediation effects of three kinds of native quinoa in a desert mining area were studied. We used two different types of local soils (native soil and tailing soil) to analyze the changes in the heavy metal content, leaf physiology, photosynthetic parameters, stem hydraulics, and anatomical characteristics of potted quinoa. The results show that the chlorophyll content, photosynthetic rate, stomatal conductance, and transpiration rate of Kochia scoparia were decreased, but intercellular CO2 concentration (Ci) was increased under heavy metal stress, and the net photosynthetic rate (Pn) was decreased due to non-stomatal limitation. The gas exchange of Chenopodium glaucum and Atriplex centralasiatica showed a decrease in Pn, stomatal conductance (Gs), and transpiration rate (E) due to stomatal limitation. The three species showed a similar change in heavy metal content; they all showed elevated hydraulic parameters, decreased vessel density, and significantly thickened vessel walls under heavy metal stress. Physiological indicators such as proline content and activity of superoxide dismutase (SOD) and peroxidase (POD) increased, but the content of malondialdehyde (MDA) and glutathione (GSH), as well as catalase (CAT) activity, decreased in these three plants. Therefore, it can be concluded that these three species of quinoa, possibly the most dominant 30 desert plants in the region, showed a good adaptability and accumulation capacity under the pressure of heavy metal stress, and these plants can be good candidates for tailings remediation in the Jinchang desert mining area.