NSUN5, a conserved RNA 5-methylcytosine methyltransferase, promotes hepatocellular carcinoma (HCC) progression by modulating the ZBED3/Wnt/β-catenin signaling pathway. This study demonstrates that NSUN5 is significantly upregulated in HCC tissues, correlating with poor clinical outcomes. NSUN5 knockdown inhibits HCC cell proliferation, while overexpression promotes it. Using methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA immunoprecipitation sequencing (RIP-seq), the study identifies ZBED3 as a novel downstream target of NSUN5. ZBED3 overexpression counteracts the tumor-suppressive effects of NSUN5 knockdown and restores the Wnt/β-catenin signaling pathway. These findings reveal that NSUN5 promotes HCC development through the ZBED3/Wnt/β-catenin pathway, offering a potential therapeutic target for HCC treatment. The study highlights the oncogenic role of NSUN5 in HCC and identifies ZBED3 as a key mediator in this process. NSUN5 knockdown reduces ZBED3 expression and m5C modification, while NSUN5 overexpression increases it. ZBED3 overexpression rescues the tumor-suppressive effect of NSUN5 knockdown, indicating its critical role in HCC progression. The study also shows that NSUN5 is associated with tumor progression and poor prognosis in HCC patients. NSUN5 knockdown significantly impairs HCC cell proliferation in vitro and in vivo. The results suggest that NSUN5 contributes to HCC development by modulating its target gene ZBED3 through m5C modification. The study provides new insights into the molecular mechanisms underlying NSUN5-mediated HCC progression and identifies ZBED3 as a potential therapeutic target for HCC treatment.NSUN5, a conserved RNA 5-methylcytosine methyltransferase, promotes hepatocellular carcinoma (HCC) progression by modulating the ZBED3/Wnt/β-catenin signaling pathway. This study demonstrates that NSUN5 is significantly upregulated in HCC tissues, correlating with poor clinical outcomes. NSUN5 knockdown inhibits HCC cell proliferation, while overexpression promotes it. Using methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA immunoprecipitation sequencing (RIP-seq), the study identifies ZBED3 as a novel downstream target of NSUN5. ZBED3 overexpression counteracts the tumor-suppressive effects of NSUN5 knockdown and restores the Wnt/β-catenin signaling pathway. These findings reveal that NSUN5 promotes HCC development through the ZBED3/Wnt/β-catenin pathway, offering a potential therapeutic target for HCC treatment. The study highlights the oncogenic role of NSUN5 in HCC and identifies ZBED3 as a key mediator in this process. NSUN5 knockdown reduces ZBED3 expression and m5C modification, while NSUN5 overexpression increases it. ZBED3 overexpression rescues the tumor-suppressive effect of NSUN5 knockdown, indicating its critical role in HCC progression. The study also shows that NSUN5 is associated with tumor progression and poor prognosis in HCC patients. NSUN5 knockdown significantly impairs HCC cell proliferation in vitro and in vivo. The results suggest that NSUN5 contributes to HCC development by modulating its target gene ZBED3 through m5C modification. The study provides new insights into the molecular mechanisms underlying NSUN5-mediated HCC progression and identifies ZBED3 as a potential therapeutic target for HCC treatment.