Studies have shown that abnormal mitochondrial function is closely associated with the development and progression of colorectal cancer (CRC); however, prognostic models based on mitochondria-related genes are still lacking. We systematically analyzed the expression of mitochondrial-related genes in CRC patients and constructed and validated a mitochondrial gene risk prognostic model using various bioinformatics methods across the TCGA and GEO databases. We also investigated the effects of tumor microenvironment, immune cell infiltration, tumor mutation load, and drug sensitivity on patient prognosis. In addition, we overexpressed the ABCD3 gene using CRISPR-dCas9 technology and further explored the role of ABCD3 in cell proliferation and apoptosis by protein blotting and flow cytometry. The mitochondrial gene risk model was effective in predicting the prognosis of CRC patients, which showed that the high-risk group was significantly different from the low-risk group in terms of immune cell infiltration. Further analyses revealed a strong association between risk scores and clinicopathological features, immune infiltration, and drug sensitivity. We constructed a prognostic prediction model based on mitochondria-related genes and found that ABCD3 provides a novel biomarker for the individualized treatment of CRC.