In winter wheat-summer maize double cropping, fertilization changes the nitrogen (N) balance in the soil N pool, grain N uptake, N loss, and nitrogen use efficiency (NUE), ultimately impacting crop productivity and environmental health. For agricultural systems to maintain yields at lower environmental costs, N budgets must be balanced. Still, there is a deficiency in the reporting of N budgets of farming systems that incorporate all N flows. We evaluated the effects of various N fertilizer application rates on soil N balance and crop productivity in the 2017–2021 winter wheat-summer maize growing seasons. These rates included non-N fertilization (N0), 75 kg·N·ha−1 (N75), 150 kg·N·ha−1 (N150), 225 kg·N·ha−1 (N225), and conventional N fertilizer application rate, 300 kg·N·ha−1 (N300). Our analysis was based on a long-term field fertilization experiment and in-situ observation (established in 2010). The results show that fertilization significantly increased crop yields (wheat: 29.2 %–97.6 %; maize:25.4 %–98.1 %; annal: 27.0 %–96.7 %), among which N225 showed the highest increase value, compared with N0. Moreover, the N225 maximized grain N uptake by 201.0 %, reducing N losses and increasing N sequestration compared to the conventional N application rate of N300. N balance changes from negative to positive as the N application rate increases (wheat: −63.78–85.24 kg·ha−1; maize: −55.77–82.25 kg·ha−1; annal: −119.58–167.46 kg·ha−1·yr−1). Combining years of N inputs and outputs, the N225 is more balanced. Therefore, our study shows that an appropriate reduction of N fertilizer (N225) can help maintain agricultural productivity and promote N sequestration in farmland by reducing environmental N loss. Maintaining the virtuous cycle of N in the farmland ecosystem is beneficial and essential for the efficient utilization, high yield, and sustainable development of farmland resources.