<p>Horticultural products play an increasingly vital role in addressing the nutritional needs of the world��s expanding population, which has surpassed 8 billion. The global trend towards health-oriented diets has motivated consumers to seek high-quality natural horticultural food consumption. This highlights the pressing requirement for updated guidance and strategies for sustainable horticultural quality upgrading. Meanwhile, DNA methylation, an epigenetic modification having transcriptional-regulation potential, is emerging as a crucial quality dominator of horticultural food. In this current investigation, we integrate valuable methylation loci regulating quality traits in fruit and vegetable, elucidating the underlying mechanisms and emphasizing the impressive species-specificity. At this early stage, the most extensively studied aspects of DNA methylation include promoter methylation and transposable elements. Additionally, we delve into locus-specific methylation-editing techniques, whose achievable genetic-modification-free advantages are promising to alleviate consumer concerns regarding genetic-modification products. Overall, this review is devoted to providing insights into the sustainable development of horticultural produce and food quality design strategies in response to global food quality and security challenges.</p>