Epigenetics plays a crucial role in various clinical diseases, such as autism, by mediating the impact of environmental variables on genomic regulation. Autism spectrum disorder (ASD) is a neurological disorder influenced by both genetic and environmental factors that affect the developing brain. DNA methylation, histone tail modifications, and non-coding RNA activity can change the function of genes without altering nucleotide sequences. Genes and environment combine to produce the etiology of ASD. One of the main areas of ASD research now being studied is the effects of epigenetic factors on gene expression, such as DNA methylation. Autistic patients exhibit evidence of oxidative stress and impaired methylation, which may reflect the effects of toxic exposure on sulfur metabolism that may lead to cellular damage in the brain and altered expression of epigenetic genes. This review paper summarizes the findings of the supplementary therapy studies of ASD, showing that supplements, including B9, B12, B6, D, E, C, glutathione, omega-3, and choline, are highly effective in modifying methylation in autism, improving many nutrient and metabolic problems, and resulting in significant improvements in symptoms.