It is all known that molecular marker-assisted selection (MAS) technology provided a new method for rice breeding. Integrated with traditional breeding technology, breeding efficiency was enhanced and breeding periodic time was reduced markedly. To potentiate the application of MAS was greatly significant in rice breeding. In this essay, we summarized the characteristics and types of molecular marker,introduced the basic principle of the marker-assisted selection, focused on its application in rice breeding, such as backcross breeding, gene polymerization and improving quantitative traits. At the same time, the problems and potential prospects of molecular marker-assisted selection have also been discussed.