Understanding the effect of carbon dioxide (CO₂) modified atmosphere packaging (MAP) on postharvest quality and its molecular mechanism in peanuts will be helpful for the application and optimization of CO₂-MAP. The appearance quality, lipid oxidation indices (acid value, carbonyl value, and malondialdehyde content), DPPH free radical scavenging rate, and the activity of superoxide dismutase (SOD) and lipoxygenase (LOX) of fresh edible peanuts packaged with CO₂ or air (CK, control group) were determined at 7 d intervals for 35 d. Transcriptome sequencing (RNA-seq) of peanuts was performed to identify differentially expressed genes (DEGs) and enriched functional pathways. CO₂-MAP could maintain the appearance quality of peanut pods and kernels. Compared with the control, CO₂-MAP maintained a lower acid value (14.3% lower), carbonyl value (10.7% lower), and malondialdehyde content (22.5% lower), suppressed LOX activity (23.4% lower), as well as retained higher DPPH radical scavenging activity (31.1% higher) and SOD activity (25.0% higher) at 35 d. Transcriptomics identified 3575 downregulated and 2166 upregulated DEGs between the CO₂-MAP and CK. These DEGs were significantly enriched in pathways related to energy metabolism, carbon metabolism, lipid metabolism, signal transduction, and antioxidant functions. Collectively, CO₂-MAP effectively delayed quality deterioration of peanuts by suppressing lipid oxidation, enhancing antioxidant capacity, reprogramming energy metabolism, and attenuating senescence-associated signaling pathways.