Water and nutrition are mainly uptaken by the root system, and the root system is directly grown in the soil and is sensitive to stress. In arid environments, the structure of the root system could be changed to maintain normal biology function and adapt to stress conditions. To date, most of the studies have focused on the structure or morphology of root system responses to single stress factors. However, less attention has been concentrated on the adaptive mechanism of the entire root structure to different ecotopes. Therefore, this study explored the root morphological plasticity of Ziziphus jujuba var. spinosa in response to natural drought gradient ecotopes. Root samples were selected from Yantai-Shijiazhuang-Yinchuan-Turpan of China. The four ecotopes formed a natural drought gradient environment according to their soil moisture, annual precipitation, and humidity coefficients. The purpose of this study was to elucidate the mechanism of root plasticity response to different environments caused by climate change. The results showed that root primary structure of Ziziphus jujuba var. spinosa included the epidermis, cortex, and vascular cylinder. The epidermis is on the surface of the young root, which is constituted by a single layer of epidermis cells that are small and arranged closely. The cortex takes the greatest proportion of the primary structure, and it is constituted by a larger quantity of parenchymal cells. The vascular cylinder is located in the innermost layer, and the cells are small and crowded together. It is composed of pericycle, primary xylem, primary phloem, and parenchymal cells. When drought aggravated, the thickness and width of the epidermis cells were increased. In addition, the thickness, width, and number of plies of parenchymal cells, and the thickness of the cortex were all largest at the Yinchuan ecotope. The root secondary structure of Ziziphus jujuba var. spinosa was divided into periderm (phellem layer, phellogen, phelloderm) and secondary vascular tissue (secondary phloem, vascular cambium, secondary xylem). As the drought intensified from Yantai to Turpan, the thickness and density of periderm was gradually increased. In addition, the diameter and quantity of vessels in secondary xylem were increased. These results illustrated that one of the adaptive mechanisms of plant to drought stress is the changes in the plasticity of root structure that enhance water uptake capacity and water transport efficiency. On the other hand, it improves water retaining capacity and decreases water desorption.