Liver injury is a major health issue with significant implications for liver function and overall well-being, but precise mechanisms of the N-methyladenine (mA) reader YTHDF3 in liver injury remain severely understudied. Here, we discovered that Ythdf3 knockout exacerbated CCL-induced liver injury with a reduction in functional hepatocytes and liver stem cells using single cell RNA-sequencing and organoid culture. Furthermore, Mettl14 and YTHDF3-dependent RNA mA dysregulation induced DNA damage. Moreover, we found YTHDF3 could bind and modulate CCAAT/enhancer-binding protein-alpha (CEBPA) translation in an mA-dependent manner. Mechanistically, knockout of Ythdf3 impeded the translation of CEBPA, subsequently inhibiting the expression of poly(ADP-ribose) (PAR) polymerase-1 (PARP1) and Peroxiredoxin 2 (PRDX2). This inhibition promoted DNA damage and genomic instability, ultimately exacerbating liver damage. This work uncovers an essential role of mA/YTHDF3/CEBPA regulatory axes in governing cell fates and genomic stability, thereby preventing liver injury. Importantly, these findings offer potential therapeutic avenues for targeting YTHDF3 and CEBPA in the treatment of liver injury-related diseases.