Background: In the process of long-term carcinogenesis, cells accumulate many mutations. Deregulated genes expression causes profound changes in cell proliferation, which is one of the hallmarks of HCC. Comprehensive understanding of these changes will contribute to the molecular mechanism of HCC progression. Methods: Western blot and real-time PCR analyses were performed to examine the TMEM220 expression in HCC. Patients’ transcript profiling was used to identify gene cohorts related to TMEM220. Reverse phase protein arrays (RPPA) were preformed to obtain expression data for TMEM220 relevant proteins. The effect of TMEM220 on tumor growth and metastasis were analyzed by in vitro and in vivo studies.Results: Through clinical sample analysis, we found that TMEM220 is downregulated in tumor and lower levels of TMEM220 is associated with poor prognosis in HCC patients. Through overexpressing TMEM220 in HCC cell lines, we found that the proliferation of cancer cells was significantly slowed down and metastasis was significantly reduced. For further study of its molecular mechanism, we performed Reverse Phase Protein Array (RPPA). The results suggest that phenotypic changes caused by TMEM220 in HCC cells might be associated with FOXO and PI3K-Akt pathways. Mechanism studies showed that overexpression of TMEM220 could regulate β-catenin and FOXO3 transcriptional activity by altering their subcellular localization, affecting the expression of downstream gene p21 and SNAIL, and ultimately reducing the progression of HCC. Conclusion: Altogether, our study proposes a working model in which upregulation of TMEM220 expression alters the genes expression involved in cell proliferation, thereby inhibiting HCC progression, which suggests that TMEM220 might serve as a clinical biomarker.