A better understanding of the effects of irrigation model on soil nutrients is important to agronomists and farmers for developing management packages with high-yield, good-quality and low water and fertilizer applications. A pot-based experiment with winter wheat cultivar (Triticum aestivum L.) was conducted under rainproof shelter during the growing seasons of 2012—2013 and 2013—2014 to investigate the effects of regulated deficit irrigation (RDI) on nitrogen, phosphorus and potassium uptake and utilizations in Xinxiang City of Henan Province, in the Huang-Huai-Hai Plain of China. The experimental treatments included five growth stages (I, three leaves-winter;II, winter-beginning of spring growth;III, beginning of spring growth-stem elongation;IV, stem elongation-ear emergence and V, ear emergence-maturity) and three levels of water deficit (60%~65% FC (field capacity), 50%~55% FC, and 40%~45% FC for light, moderate, and severe deficit, respectively) were laid out in a randomised complete block design with three replicates. A non-deficit control (CK) (75%~85% FC from sowing to maturity) with three replications was also included. The results indicated that light or moderate water deficit at winter-beginning of spring growth stage benefited nutrients translocation and distribution in the grains, and excess of water in the soil or inapplicable water deficit resulted in increase of proportion of nutrients accumulation in vegetative organs. Appropriate water deficit (50%~55% FC) during ear emergence-filling stage was able to increase nitrogen and phosphorus contents in grains, and then increase grain yield and improve quality. Light water deficit or moderate water deficit during beginning of spring growth-stem elongation stage was favorable to improve nitrogen and phosphorus use efficiencies, but water deficit at any stages was unfavorable to increase potassium use efficiency. The results also showed that appropriate water deficit (especially light water deficit at winter stage or moderate water deficit at stem elongation stage) significantly enhanced nitrogen absorption ability of plants from soil, and reduced nitrogen residue in soil. Therefore, it was suggested that RDI can effectively regulate nitrogen, phosphorus and potassium uptake, and promote water and fertilizer savings, high yield, good quality and high efficiency of winter wheat.