The extreme climate affairs occur more frequently under the trends of global warming. Heat has been one of the major constrains of rice yield and quality. The most effective way to solve the problem is to develop new rice varieties with heat tolerance. The advance of molecular biotechnology and rice functional genome research provide an effective approach for studying on the genetic bases of rice heat tolerance. The damage mechanism of heat stress and genetic basis of heat tolerance in rice were summarized in this review, e.g. QTL mapping and cloning, transcriptome and proteomics. It may facilitate the deep dissection of genetic mechanism of heat tolerance in rice and the development of new rice variety with heat tolerance.