Vitamins are essential metabolic cofactors, yet their roles in epitranscriptomic regulation, particularly N⁶-methyladenosine (m⁶A) modification, remain unclear. Here, we investigate the effects of various vitamins (VB2, VB6, and VB12) on the mRNA m⁶A epitranscriptome in multiple mouse tissues (brain, liver, and testis). Clustering analyses reveal closer similarity between the brain and testis m⁶A profiles, whereas the liver exhibits a unique pattern, reflecting tissue-specific regulatory dynamics. More than 90% of m⁶A sites are independent of mRNA abundance, highlighting the post-transcriptional role of m⁶A modification. Additionally, alternative splicing (AS) variations reveal complex interactions between vitamins, m⁶A modification, and AS, with tissue- and vitamin-specific effects on biological pathways. We identify 22 comethylation modules, associated with pathways such as neurodegenerative diseases and immune regulation. Key vitamin-responsive genes are found as central regulators of m⁶A dynamics, aligning with known roles of vitamins in metabolism, neural plasticity, and gene expression. Together, our findings provide the first comprehensive atlas of vitamin-driven, tissue-specific m⁶A modifications, offering new insights into the post-transcriptional regulatory mechanisms underlying vitamin-mediated cellular functions and their implications for nutritional or pharmacological modulation of the epitranscriptome in health and disease.