Abstract: Open-pit mining of coal mines in arid and semi-arid areas destroys surface morphology, accelerates soil water loss, and the lack of water resources seriously affects the effect of vegetation restoration in open pit dump. Soil reconstruction technology and microbial remediation technology point out the direction to solve the water shortage dilemma of vegetation in open pit dump, but the relationship between plant root morphological characteristics and soil water use efficiency under soil reconfiguration and the important role of dark septum endophytic fungi (DSE) in soil reconfiguration are not well understood. The purpose of this study was to explore the root growth and water use of maize under soil layer reconstruction mode, as well as the mechanism of DSE. The study object was maize, and the soil layer reconstruction experiment was simulated in a greenhouse for 4 months. The experiment was arranged in three groups: blank control(N-CK), soil layer reconstruction without DSE inoculation(L-CK), soil layer reconstruction with DSE inoculation(L-DSE). The results showed that: ① Compared with blank control treatment, the total root length of maize root system under soil layer reconstruction treatment was reduced by 39.7%, the proportion of fine roots less than 0.3mm in the root system was increased by 8.86%, and the water use efficiency of deep (50−70 cm) soil was increased by 16.1%. ② Compared with the reconstructed soil layer without DSE inoculation, the proline content in leaves of maize inoculated with DSE increased by 69.8%, the number of root tips and specific root length in 30−50 cm soil layer increased by 106.6% and 38.5%, respectively. In addition, the water use efficiency in deep soil increased by 29.3% and 11.1%, respectively, compared with that of N-CK and L-CK. ③ Root tip number and fine root volume of the maize root system are the key root characteristics to achieve efficient use of soil water under the soil layer reconstruction model. The combined study showed that soil layer reconstruction was helpful to optimize the root structure of maize, increase the proportion of fine roots and the number of root tips, and improve the water use pattern of maize under water shortage environment, and DSE inoculation under the soil layer reconfiguration model could improve the use rate of deep soil water by increasing the content of proline in leaves and optimizing the structure of maize root system, so as to improve the long-term drought resistance of crops.