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Nitrogen (N) plays a vital role in plant growth; however, the yield response to N fertilizer is regularly declining in the major cropping systems due to overuse and the upper limit of yields. Heavy losses of N are also documented due to its excessive use in the rice-wheat rotation system, resulting in low nitrogen-use efficiencies (NUE) and environmental problems. Therefore, a three-year field experiment was performed with different N managements to investigate the impact of reduced N input rates in this exhaustive cropping system. Reducing the N application rates did not affect the wheat and rice yields significantly, only during the second wheat season was the yield slightly reduced as compared to higher N input treatments. Decreasing the N input rates in the prior crop and present crop, and the interactions of both rice and wheat seasons (R × W) did not influence the yields of either crop. A reduction in N fertilizer had a considerable impact on dry matter production during the wheat seasons but demonstrated no effect during the rice season. The accumulation of N was significantly reduced during both crop seasons by lowering the rate of N application. In addition, the NUE indices were significantly influenced by N fertilizer application rates. In conclusion, N fertilizer input rates for both rice and wheat crops can be lowered as compared to present fertilization rates without any risk of yield decline. Lowering the N input increases the NUE and effectively reduces N losses, and soil N status can also be maintained.