Under the current situation, paddy soils are generally overused with nitrogen fertilizer, and nitrogen use efficiency of rice is not high in China, so we expounded the physiological mechanisms of genotypic differences of nitrogen use efficiency and summarized the research progresses at the molecular biology perspective in rice. Nitrogen use efficiency of rice is restricted by many factors, and the difference among rice varieties is a key factor that restricts actual production, its effect on rice nitrogen nutrition characteristics is mainly reflected in rice yield formation, photosynthetic and root biological characteristics. In-depth researches for these are favorable to optimize the source-sink relationship at each stage of rice growth. The processes of absorption, transportation and assimilation for different nitrogen patterns in rice are executed by associated transporters and enzymes. Research on molecular mechanism will provide the coordination between nitrogen use efficiency for biomass production and source-sink relationship of rice. In addition, nitrogen assimilation needs to consume energy and carbon skeletons, so enhancing the intensity of leaf photosynthetic carbon assimilation can drive nitrogen allocation more rationally for the plant, which is beneficial to improve nitrogen use efficiency. Many attempts have been made to regulate rice nitrogen utilization by applying rice genotypic differences and the genetic manipulation. In the future, we should make full use of the functional characteristics of its multiple genetic locus, as well as increasing carbon provision to enhance the strength of the leaf as a source organ that provides the photosynthesis product, which is more effective to coordinate the source-sink relationship. Besides, the physiological mechanisms of these processes should be explored deeply. It is expected to provide foothold for improving the current nitrogen use efficiency and promoting production of rice.