Spinal cord injury (SCI) represents a profound neurological condition characterized by motor dysfunction and sensory impairment. Microglial polarization significantly influences neurorepair and regeneration post SCI. This study aims to investigate the regulatory role of the ELAV-like RNA binding protein 1 (ELAVL1)-ubiquitin-specific peptidase 29 (USP29)-transforming growth factor beta-activated kinase 1 (TAK1) axis in microglial polarization and its effects on differentiation of neural stem cells (NSCs). A rat model of SCI was established via spinal cord transection at the tenth thoracic vertebra segment, followed by short hairpin RNA (shRNA) lentivirus infection. Motor function and coordination were evaluated while histopathological analysis of spinal cord tissues was conducted. Microglial polarization and NSC differentiation were assessed via immunofluorescence and Western blot analysis. In cellular experiments, lipopolysaccharide (LPS) was utilized to induce M1 polarization in HMC3 cells, with polarization status determined by flow cytometry, immunofluorescence, and WB. Co-immunoprecipitation, GST pull-down, and ubiquitination assays elucidated USP29 effects on TAK1 ubiquitination and activation. In SCI rat spinal cord tissues and LPS-treated HMC3 cells, we observed upregulation of ELAVL1 and phosphorylated level of TAK1, while USP29 expression was downregulated. ELAVL1 was found to bind USP29 mRNA, promoting its degradation and suppressing USP29 expression. USP29 directly interacted with TAK1, inhibiting its ubiquitination and phosphorylation. Knockdown of ELAVL1 significantly enhanced USP29 mRNA stability, inhibited TAK1 activation, promoted M2 microglial polarization, and suppressed M1 polarization. In vivo downregulation of ELAVL1 promoted the differentiation of NSCs into neurons by inhibiting M1 polarization and promoting M2 polarization, thereby improving motor function, alleviating nerve injury, and facilitating spinal cord repair. ELAVL1 exacerbates SCI pathology by degrading USP29 mRNA, thereby activating TAK1 and driving M1 microglial polarization. Targeting the ELAVL1-USP29-TAK1 axis may offer therapeutic potential for enhancing neurorepair in SCI. Schematic diagram of the ELAVL1-USP29-TAK1 axis mediating M1 microglial polarization and NSC differentiation dysregulation exacerbating SCI.