In this research, the effect of CO2 (0%, 20%, 60%, and 100%) on the spoilage potential of Shewanella putrefaciens (S. putrefaciens) during 4 °C cold storage was evaluated. Results revealed that the growth curves of S. putrefaciens were effectively affected by CO2 with prolonged lag phases and delayed logarithmic phases. Protein oxidation of inoculated large yellow croakers was noticeably delayed with the treatment of CO2 by keeping higher myofibrillar protein, total sulfhydryl groups and Ca2+-ATPase activity, and lower carbonyl groups. Spatial structures of samples treated with 20%–100% CO2 were better in organized secondary structure and better-stabilized tertiary structure. Meanwhile, the myofibrillar microstructure detected by scanning electron microscope (SEM) and transmission electron microscopy (TEM) was also much well-organized than the control, with relative tightly attached myofibrils and intact sarcomere structure (clear A-band, I-band and M-lines). Furthermore, CO2 treated samples have better texture and stronger moisture holding capacity. These results synergistically demonstrated that the spoilage ability of S. putrefaciens target at proteins was effectively suppressed by CO2.