Soil management practices are important parts of sustainable agriculture. Improving tillage practice is important for alleviating soil degradation and promoting sustainable grain production. A four year field experiment was conducted to examine the effects of deep tillage (DT), incorporated into the minimum tillage (MT), on soil physical properties and crop performance. The field experiments included continuous rotary tillage (RT), continuous DT, and intermittent DT every three years, every two years, and every other year, into RT. The results showed that the introduction of DT into continuous RT reduced the soil bulk density of the 20–30 cm soil layer by 5.6% and reduced nutrient stratification rates by 20–30%, which favored more uniformly distributed soil nutrients in the top soil layer. The root growth for treatments with DT in the deep soil layers (1–1.5 m) was significantly improved, which resulted in a higher soil water depletion. Under deficit irrigation scheduling, the improved root growth and soil water uptake in the deep soil layer improved crop growth and grain production. Overall, a 10.5% increase in yield and 18.3% increase in water productivity were observed when intermittent DT was introduced during the four years. The effects of DT could be maintained for two continuous years. Therefore, it was suggested that after two or three years of RT, DT should be applied to improve soil physical properties and ensure high grain production.