N fertilizer application plays an important role in maintaining food security in China. However, over-application of N fertilizer results in the reduction in nitrogen use efficiency (NUE) and a series of environmental problems. Simultaneous increase in yield and NUE has been a big challenge in agricultural production since 21st century, and attracted lots of research endeavors. Here, we introduced the rational and technique of typical N fertilizer management practices; summarized the progress in high NUE rice breeding, especially the Green Super Rice; reviewed the physiological and molecular mechanisms of high NUE, focusing on the effect of nitrogen on photosynthetic physiology and the important genes regulating NUE.