Bilirubin-induced brain damage represents a serious clinical consequence of hyperbilirubinemia, yet the role and underlying molecular mechanisms of autophagy the remain largely elusive. Here, we demonstrate that, for the first time, N6-methyladenosine (m6A) demethylase AlkB homolog 5 (ALKBH5) mediated dysregulated autophagic flux contributes to bilirubin-induced neurotoxicity. Hyperdifferential differentiated PC12 cells and neonatal Sprague-Dawley rats were employed as in vitro and in vivo models, respectively. In vivo experiments first showed a dysregulated autophagy and neuronal damage in hyperbilirubinemia. In vitro further experiments observed that bilirubin exposure inhibited autophagy as illustrated by the downregulated p62 and LC3-II protein expression and transmission electron microscopy results. Furthermore, we found that the autophagic flux impairment was due to the inhibition of initial stage following bilirubin exposure, which was pharmacologically validated using rapamycin and bafilomycin A1 and up-regulated protein expression of p-mTOR and BCL2. More importantly, we found that ALKBH5 overexpression can exacerbate bilirubin-induced autophagic flux damage, whereas ALKBH5 knockdown attenuated the inhibited autophagic flux damage. Mechanistically, Vacuole membrane protein 1 (VMP1), Ras-related GTP-binding protein C (RRAGC), and protein kinase AMP-activated catalytic subunit alpha 1 (PRKAA1) were identified as the target genes of ALKBH5 to impair autophagic flux with mRNA stability assay, RT-PCR analysis, and bioinfomatic analysis, thereby promoting bilirubin-induced neurotoxicity. Collectively, our findings reveal that ALKBH5 participates in bilirubin-induced autophagic flux impairment, and propose m6A-dependent autophagy as a potential therapeutic target in hyperbilirubinemia.