Background Mitochondrial-related genes (MRGs) and programmed cell death-related genes (PCD-RGs) have been proven to play important roles in obsessive-compulsive disorder (OCD), and identifying their shared biomarkers is conducive to the diagnosis and research of OCD. Methods Differentially expressed genes (DEGs) between OCD and control samples were identified from the GSE78104 dataset. Differentially expressed MRGs (DE MRGs) and PCD-RGs (DE-PCD-RGs) were derived by intersecting with MRG and PCD-RG gene sets, respectively, resulting in DE mitochondrial-related PCD (DE-MPCD) genes. Key OCD-related genes were identified using weighted gene co-expression network analysis (WGCNA), and candidate genes for OCD were selected by intersecting these with DE-MPCD-RGs. Machine learning algorithms were applied to further screen potential biomarkers from the GSE78104 and GSE60190 datasets. The expression levels of selected biomarkers were validated using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in samples from patients with OCD and healthy controls to assess the mRNA expression. Gene Set Enrichment Analysis (GSEA) was conducted to identify enriched pathways in these biomarkers. Immune cell infiltration patterns in OCD and potential therapeutic agents were also investigated. Results A total of 13 DE-MPCD-RGs were intersected with 374 key module genes, resulting in 12 candidate genes. Among these, eight potential biomarkers for OCD were identified. Notably, NDUFA1 and COX7C were significantly downregulated in OCD across both datasets and clinical samples, establishing them as reliable biomarkers for OCD. GSEA revealed that NDUFA1 and COX7C were significantly co-enriched in pathways such as "ribosome," "oxidative phosphorylation," "phosphorylation," and "Parkinson's disease." Furthermore, activated CD8 T cells and neutrophils were identified as the differential immune cell types between OCD and control samples. Additionally, 73 potential therapeutic agents were predicted through drug-target interaction analysis. Conclusion This study identified two mitochondrial-related biomarkers in OCD, providing novel perspectives on the disorder's pathogenesis. These findings hold promise for advancing early diagnosis and the development of targeted therapeutic strategies for OCD.