Global warming poses a significant threat to plant ecosystems and agricultural productivity, primarily through heat stress (HS), which disrupts photosynthesis, respiration, and overall plant metabolism. Epigenetic modifications, including DNA methylation, histone modifications, and RNA modifications, enable plants to dynamically and heritably adjust gene expression in response to environmental stressors. These mechanisms not only help plants survive immediate stress but also confer stress memory, enhancing their resilience to future HS events. This review explores the mechanisms underlying plant thermotolerance, emphasizing the critical role of epigenetic regulation in adapting to HS. It also highlights how DNA methylation modulates stress-responsive genes, histone modifications facilitate transcriptional memory, and RNA modifications influence mRNA stability and translation. Recent advancements in genome editing technologies, such as CRISPR-Cas9, have enabled precise modifications of epigenetic traits, offering new avenues for breeding climate-resilient crops. The integration of these modern tools with traditional breeding methods holds significant promise for developing crops with enhanced thermotolerance. Despite the potential, challenges such as the stability and heritability of epigenetic marks and the complex interplay between different epigenetic modifications need to be addressed. Future research should focus on elucidating these interactions and identifying reliable epigenetic markers for selection. By leveraging the insights gained from epigenetic studies, we can develop innovative breeding strategies to improve crop resilience and ensure sustainable agricultural productivity in the face of global warming. This review underscores the importance of epigenetic regulation in plant adaptation to heat stress and its potential to revolutionize crop breeding, offering a pathway to secure food production and sustainability under changing climatic conditions.