Owing to their sessile nature, plants have to passively respond to daily and seasonal temperature changes. Plants have evolved sophisticated genetic and epigenetic regulatory systems to perceive the ambient temperature and adjust the growth and development to survive. Global warming has posed a serious threat to the global food supply. It is of great urgency to investigate the molecular mechanism of heat stress response in plants. DNA methylation, histone modification, chromatin remodeling and small RNAs are major epigenetic regulation mechanisms. These epigenetic modifications have their own roles and work together in regulating the thermotolerance of plants. In this review, we summarized recent published researches on the epigenetic regulation of heat stress response in plants.