The aim of this study was to assess the prognostic value of the multi-PDZ domain protein (MPDZ) in hepatocellular carcinoma (HCC). MPDZ expression in HCC and normal liver tissue samples were analyzed using TCGA-LIHC data and validated in the GSE14520, GSE62232, GSE76427, GSE121248, and GSE136247 datasets. MPDZ's prognostic value in HCC was evaluated based on Kaplan-Meier survival analysis and Cox proportional risk models. The correlation of MPDZ with other prognostic factors was explored by combined survival analysis and stratified survival analysis. The differentially expressed genes between patient groups stratified on the basis of MPDZ levels in TCGA-LIHC were screened using R and functionally annotated by the GO and KEGG pathway analysis by DAVID. Furthermore, gene set enrichment analysis was conducted to determine the basic molecular mechanism of MPDZ in HCC, and the protein-protein interactions, gene-gene interactions, and immune infiltration status of MPDZ was analyzed by STRING, GeneMania, and TIMER. Our findings indicate that MPDZ is downregulated in HCC and portends worse prognosis. Bioinformatics analysis revealed a strong link between MPDZ and liver cancer progression, liver cancer survival, multiple metabolic pathways, and multiple signaling pathways. In addition, our findings indicate that MPDZ expression is associated with several key genes in the ferroptosis pathway and m6A methylation. Finally, immunohistochemical assessment of clinical specimens confirmed low MPDZ protein expression in HCC tissues relative to paraneoplastic tissues. Taken together, MPDZ is a promising biomarker for the diagnosis and prognosis of HCC.