The study was carried out in Shenzhou Experimental Station, Arid Farming Research Institute, Hebei Academy of Agricultural and Forestry Sciences in 2012–2013. The maize variety Zhengdan 958 was used in this experiment with two treatments including sub-soiling seeding (SRT) and no-tillage seeding(NT). From seedling emergence to maturity, the root morphology, physiological parameters and microstructure, canopy photosynthetic characteristics, and leaf area index were regularly measured. At maturity, the yields and the water use efficiency and water storage in 2 m soil layer were investigated. The results showed that SRT increased the root dry mass, surface area, length and active absoiling area ratio in 0–60 cm soil layer, with the increase of 30.5%, 24.6%, 29.7%, and 56.3%,respectively, in comparison with NT. In addition, SRT also increased the proline content, nitrate reductase activity and activity of roots compared with NT in this soil layer, with the increase of 140%, 37%, and 36.5%, respectively. The total root bleeding sap in SRT increased by 15.2% compared with NT in the whole growth stage. In 0–40 cm soil layer, the hydraulic conductivity in single root and the roots per plant around whole growth stage in SRT increased by 15.8% and 17% respectively, in comparison with NT. In SRT, the diameter of stele vessel was increased, cell walls of pericycle and stele parenchyma were thickened, and the number of pith cells were increased, but its section area ratio in stale decreased compared with NT. Moreover, the numbers and diameter of xylem vessel in SRT increased, but the cortical thickness in roots decreased. In 0–20cm soil layer, although the middle cortical cells of root in SRT were larger than those of NT, but there number was only 86.2% of NT. SRT also increased the LAI and photosynthetic rate. The grain-filling rate in SRT treatment was also increased, with 5% higher than in NT. In two growth seasons, compared with NT, the spike kernels, 1000-grain weight, and yield in SRT treatment were increased by 2.4%, 3.9% and 8.2%, respectively, whereas the water consumption was reduced by 9.1%, the water use efficiency was increased by 14.4%, and the water storage amount in 2 m soil layer was increased by 31.7%.