Pseudomonas fragi is a predominant meat-borne spoilage bacterium that is sensitive to CO2 under high-oxygen modified atmosphere packaging (HiOx-MAP). This study was designed to reveal the spoilage potential of a popular wild-type P. fragi T1 in HiOx-MAP beef by whole genome sequencing, and explore the bacterial metabolic response to CO2 utilizing combined metabolomic and volatile organic compounds (VOCs) analysis, under treatment (CO2-enriched) HiOx-MAP (TMAP, 50% O2/40% CO2/10% N2) or control (non-CO2) HiOx-MAP (CMAP, 50% O2/50% N2) during chilled storage. Results showed that the strain P. fragi T1 was endued with spoilage-related genes associated with protease, lipase and esterase production, amino acid metabolism, carbon metabolism, sulfur metabolism, and putrescine metabolism, which was responsible for the hydrolysis of meat protein and lipid, as well as off-odor formation. The growth of P. fragi under CMAP resulted in the production of VOCs, such as diacetyl, 1-undecene, 2-undecanone, nonanal, (Z)-5-decen-1-ol, and (E)-2-octenal, etc. The TMAP declined above VOCs concentrations significantly (P < 0.05) by inhibiting P. fragi growth and regulating its metabolic activities. The metabolomic analysis further manifested that CO2 inhibited the P. fragi growth by decreasing cell membrane fluidity, disturbing energy metabolism, and inhibiting amino acid metabolism and nucleotide biosynthesis. This work provides valuable information for understanding the P. fragi-induced meat spoilage phenomena, and the antibacterial mechanism of CO2 against P. fragi.