AbstractRegeneration is the regrowth of damaged tissues or organs, a vital process in response to damages from primitive organisms to higher mammals. Planarian possesses active whole‐body regenerative capability owing to its vast reservoir of adult stem cells, neoblasts, providing an ideal model to delineate the underlying mechanisms for regeneration. RNAN6‐methyladenosine (m6A) modification participates in many biological processes, including stem cell self‐renewal and differentiation, in particular the regeneration of haematopoietic stem cells and axons. However, how m6A controls regeneration at the whole‐organism level remains largely unknown. Here, we demonstrate that the depletion of m6A methyltransferase regulatory subunitwtapabolishes planarian regeneration, potentially through regulating genes related to cell–cell communication and cell cycle. Single‐cell RNA‐seq (scRNA‐seq) analysis unveils that thewtapknockdown induces a unique type of neural progenitor‐like cells (NP‐like cells), characterized by specific expression of the cell–cell communication ligandgrn. Intriguingly, the depletion of m6A‐modified transcriptsgrn,cdk9orcdk7partially rescues the defective regeneration of planarian caused bywtapknockdown. Overall, our study reveals an indispensable role of m6A modification in regulating whole‐organism regeneration.