Controlled drainage (CD) is an important agricultural measure for maintaining soil moisture and nutrients, controlling groundwater level, and increasing crop yield. In arid regions, CD can be used to improve the water supply in agriculture and reduce environmental pollution. In this study, we investigated the effect of CD, including a drainage depth of 40 cm (CWT1) and 70 cm (CWT2) during the plant growth period, free drainage (FD), and open ditch drainage (OD) on the migration of water, nutrients, and salts in the soil; the dynamics of groundwater level; the loss of soil nitrogen; and the growth of oilseed sunflower plants. Compared with FD, CD increased the water and nutrient content in the soil, reduced nitrogen loss, and enhanced the ability of the soil to continuously supply nitrogen to the oilseed sunflower plants, which benefited plant growth at later growth stages and reduced environmental pollution. During the period between irrigation at the budding stage and harvest stage, the average soil water content in the 0–20 cm soil layer in CWT1 increased by 3.67%, 4.78%, and 0.55%, respectively, compared with that in CWT2, FD, and OD. The soil mineral content in CWT1 was 25.17%, 35.05%, and 17.78% higher than that in CWT2, FD, and OD, respectively, indicating that higher soil salinity occurred at the later stage of plant growth in CWT1, which actually had little effect on the plants due to their enhanced salt tolerance and increased need for water and nutrients at that stage. In addition, CD delayed the decline in groundwater level, which allowed the plants to use groundwater at later growth stages, and as a result the yield and water use efficiency were improved. CWT1 significantly increased oilseed sunflower yield by 4.52–11.14% and increased water use efficiency by 1.16–10.8%. Moreover, CWT1 also increased the survival rate of the oilseed sunflower plants by 2.62–2.92%, and the plants demonstrated good growth. Therefore, under CD conditions, plants used soil water and nitrogen more efficiently and, as a result, their productivity was increased, and the water quality was improved.