Nitrogen (N) budgets have been computed in many countries at various scales to improve understanding of N-balance characteristics and to assess the environmental pollution risks of applying chemical fertilizer N. However, dynamic characteristics, driving forces, and potential soil fertility consequences related to cropland N balance have seldom been discussed, especially in regions with highly fertile soils and low N-use intensities. This study investigated the temporal and spatial characteristics of N balance, and the impact of agricultural development on the agro-ecosystems of the Sanjiang Plain, one of the largest producers of commodity food grains in China. County-level agricultural statistics at five-year intervals were used to calculate agricultural N balances, N surplus intensity, and N-use efficiency between 2005 and 2015. Agricultural development has brought about continual increases in cultivated land area, consumption of chemical fertilizers, and nitrogen use efficiency (NUE). Nitrogen surplus intensity decreased from 65.0 kg/ha in 2005 to 43.5 kg/ha in 2010, and to 22.2 kg/ha in 2015. However, NUE was >90% in 13 counties in 2015, and in 11 counties in 2010. In contrast, only 5 counties had NUE above 90% in 2005, which indicates that N from the soil was used by crops and soil fertility was gradually decreasing. The percentage change of crop area, namely, the increase in maize area percentage, contributed significantly to the increases in NUE. A judicious management of fertilizers that meets the nutrient needs of the crops and ensures agricultural sustainability on the Sanjiang Plain is therefore essential. The findings of this study emphasize the importance of assessing the impact of crop structure adjustment on soil fertility and nitrogen balance during agricultural development.