Improvement of the nitrogen use efficiency (NUE) positively impacts on the growth and development of plants as well as the crop productivity. In this study, we investigated the characterization on N uptake, N remobilization, and agronomic traits of winter wheat under N input treatments combined by deficit irrigation. Under the sufficient-N treatment (N240), the accumulative N amounts and internal N remobilization rates in plants of the tested cultivars (Jimai 585 and Shimai 22) were elevated relative to those under the deficient-N treatment (N120), together with improvement on plant biomass and the grain yields. Compared with Jimai 585, a control cultivar to be acclimation to affluent irrigation condition, the drought tolerant cultivar Shimai 22 enhanced the accumulative N amount, N harvest index (NHI), NUE, and agronomic traits under both N input treatments, especially under N120. In addition, Shimai 22 also displayed higher activities of nitrate reductase (NR), nitrite reductase (NIR), and glutamine synthetase (GS) than Jimai 585 under the both N level conditions. The soil N contents (NC) in 2 m profile were elevated whereas the soil moisture contents were lowered in plots planted by the wheat cultivars during late stages under N240 with respect to those under N120. Moreover, reduced soil moisture and N contents in 2 m soil profile were found in the plots grown by Shimai 22 with respect to those by Jimai 585 under N120, suggesting that Shimai 22 improved the N uptake, N remobilization, and the agronomic traits under low N input treatment to be associated with the enhanced N assimilation-related enzymatic activities and the elevated capacity for usage of the soil N storage. Therefore, it is feasible to cultivate winter wheat under the water- and N saving conditions by using the drought tolerant cultivars due to their high NUE and effective usage for the soil nutrient storage.