The nitrogen balance can serve as an indicator of the risk to the environment of nitrogen loss from agricultural land. To investigate the temporal and spatial changes in agricultural nitrogen application and its potential threat to the environment of the Haihe Basin in China, we used a database of county-level agricultural statistics to calculate agricultural nitrogen input, output, surplus intensity, and use efficiency. Chemical fertilizer nitrogen input increased by 51.7% from partly due to fertilizer composition and type improvement. This level indicates that more than half of nitrogen inputs are lost in agroecosystems. Our results suggest that although the improvement in fertilizer composition and types has partially offset the decrease in nitrogen use efficiency, the environmental risk has still increased gradually over the past 20 years, along with the increase in crop yields and nitrogen application. It is important to achieve a better nitrogen balance through more effective management to significantly reduce the environmental risk, decrease nitrogen surplus intensity, and increase nitrogen use efficiency without sacrificing crop yields.