Background:Mitophagy is the degradation of dysfunctional mitochondria. Its dysregulation can lead to an accumulation of damaged mitochondria and is implicated in carcinogenesis and tumorigenesis. Despite increasing evidence that mitophagy plays a role in colon tumorigenesis, the role of mitophagy-related genes (MRGs) in colon adenocarcinoma (COAD) prognosis and treatment remains largely unknown. Methods: As a first step, we extracted 1899 mitophagy-related genes from GeneCards and screened 461 differentially expressed genes from TCGA database. Using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis and Gene Ontology terms, we constructed a protein-protein interaction network, and conducted key module screening for the differential genes. Cox regression and least absolute shrinkage and selection operator analyses were used to identify PPARGC1A, SLC6A1, EPHB2 and PPP1R17 as prognosis-related genes. We assessed the feasibility of prognostic models using Kaplan-Meier analysis, time-dependent receiver operating characteristics, risk scores, Cox regression analysis, and principal component analysis. We tested the model using the GEO database and constructed nomograms for future clinical applications. At 1, 3, and 5 years, the area under the receiver operating characteristic curve for the TCGA cohort was 0.628, 0.678, and 0.755, whereas that of the GEO cohort was 0.609, 0.634, and 0.640. In addition, we compared immune cell infiltration between the two groups and assessed sensitivity to treatment with many commonly used chemotherapeutic agents in individuals with different risk factors. Finally, we performed qualitative reverse transcription polymerase chain reaction to examine the expression of prognosis-related MRGs. Results: In this study, we investigated the potential value of MRGs in patients with colon adenocarcinoma at the gene level. Utilizing The Cancer Genome Atlas (TCGA), we developed a mitophagy-related gene model to predict the prognosis of COAD, and examined this risk model using the Gene Expression Omnibus (GEO). Conclusions: This study has successfully constructed a mitophagy-related gene signature with significant predictive value for COAD and provides new possibilities for its future treatment.