Agricultural soils account for more than 50% of nitrogen leaching (LN) to groundwater in China. When excess levels of nitrogen accumulate in groundwater, it poses a risk of adverse health effects. Despite this recognition, estimation of LN from cropland soils in a broad spatial scale is still quite uncertain in China. The uncertainty of LN primarily stems from the shape of nitrogen leaching response to fertilizer additions (Nrate) and the role of environmental conditions. On the basis of 453 site-years at 51 sites across China, we explored the nonlinearity and variability of the response of LN to Nrate and developed an empirical statistical model to determine how environmental factors regulate the rate of N leaching (LR). The result shows that LN-Nrate relationship is convex for most crop types, and varies by local hydro-climates and soil organic carbon. Variability of air temperature explains a half (∼52%) of the spatial variation of LR. The results of model calibration and validation indicate that incorporating this empirical knowledge into a predictive model could accurately capture the variation in leaching and produce a reasonable upscaling from site to country. The fertilizer-induced LN in 2008 for China's cropland were 0.88 ± 0.23 TgN (1σ), significantly lower than the linear or uniform model, as assumed by Food and Agriculture Organization and MITERRA-EUROPE models. These results also imply that future policy to reduce N leaching from cropland needs to consider environmental variability rather than solely attempt to reduce Nrate.