Rice is the most important cereal crop in our country, the continuous and stable grain production of rice and other major crops is of great practical and strategic significance for the food security and sustainable development of agriculture. During the past 20 years, a series of important research progresses has been made in rice molecular biology and molecular design breeding, especially, with the development of new disciplines such as genomics, computational biology, systems biology and synthetic biology, the identification and utilization of important functional genes not only brings opportunity to dissect the genetic regulation network of biological complex traits, but also provides scientific basis for the innovation of breeding technology. This article briefly reviews the research progress in the studies of functional genes in associated with improvement of rice grain yield.