Nitrogen (N) use efficiency worldwide varies greatly due to climate, agronomic, and soil factors. However, the information on individual effects of these factors on N use efficiency is crucial but has remained scanty. Given that climate cannot be regulated, understanding the relative importance of fertilizer and soil variations on regional differences in N use efficiency is critical. Here, we constructed a database of 302 studies from 1986 to 2020 in East and Northeast China to determine the effects of climate, soil properties, and fertilizer N (FN) rate on variations in N use efficiency (agronomic efficiency (AE), apparent recovery efficiency (RE), physiological efficiency (PE), N harvest index, partial factor productivity), N surplus, grain N content, and reactive N (Nr) losses (N2O emissions, NH3 volatilization, Nr leaching, and runoff). Rice yield was comparable between two regions under farmers’ N practices, yet the N input was considerably higher in East China. All indices of N use efficiency, except RE, are higher in Northeast China. Differences in AE were dominated by the ability of the plant to mobilize N (PE) rather than N uptake (RE), FN, or Nr loss. Soil properties and FN related to optimizable N management accounted for 29% (RE), 39% (PE), and 43% (Nr losses) of the variations, of which key factors as pH showed a negative effect while available N (AN) correlated positively to the N use efficiency. To realize high N use efficiency, pivotal effects of pH, AN, and FN on N use efficiency under certain climate zone should be considered.