In lime concretion black soil, a two-factor (tillage and irrigation) split block experiment from 2015 to 2017 was conducted to identify whether their combination is suitable for the improvement of winter wheat yield and water use efficiency. The main treatments were subsoiling (SS) and rotary tillage (RT), with secondary treatments of three irrigation regimes: no irrigation during the whole growth period (W0), irrigation at jointing stage (W1), and irrigation at both jointing and anthesis stages (W2). In combination with a soil column experiment, the contribution of the root system in different soil layers to yield was clarified. The results indicated that both tillage and irrigation significantly influenced the spatiotemporal distributions of the root systems and yield components, while tillage produced the strongest effect. Compared with RT, SS significantly promoted the root penetration and delayed root senescence in deep soil layers. With increasing soil depth, each root configuration parameter (dry root weight density, DRWD; root length density, RLD; root surface area per unit area, RSA; root volume per unit area, RV) gradually decreased, and the peak appearance times of each root parameter in RT and three parameters (RLD, RSA and RV) in SS were postponed from heading to anthesis and from anthesis to filling stage, respectively. The average post-peak attenuation values at soil layers from 60 to 100 cm in W1 were less than those in W0 and W2. SSW1 generated the highest grain yields, with an average increase of 31.88% compared with the yield in RTW0. Root systems at three soil layers (0-40 cm, 40-80 cm and below 80 cm) differentially contributed to grain yields with 78.32%, 12.09% and 9.59%, respectively. The growth peak of the deep root system in SSW1 was postponed to the filling stage, and the post-peak attenuation declining rates were also slowed. Therefore, SSW1 is an effective cultivation method improving grain yields and water use efficiency in lime concretion black soil.