The effect of gas ratio on the growth of bacteria has been well demonstrated, but some adverse effects of modified atmosphere packaging (MAP) on seafoods have also been found. To provide a better understanding of the effects of CO2 and O2 concentrations (CO2 from 40% to 100% and O2 from 0% to 30%) in MAP on the texture and protein contents and odor characteristics of salmon during cold storage, the physiochemical, microbial, and odor indicators were compared with those without treatment (CK). Generally, MAP treatments hindered the increase of microbial counts, total volatile basic nitrogen, and TCA-soluble peptides, and decreased the water-holding capacity, hardness, springiness, and sarcoplasmic and myofibrillar protein contents. The results also indicated that 60%CO2/10%O2/30%N2 was optimal and decreased the total mesophilic bacterial counts by 2.8 log cfu/g in comparison with CK on day 12. In agreement, the concentration of CO2 of 60% showed the lowest myofibrillar protein degradation, and less subsequent loss of hardness. The electronic nose characteristics analysis indicated that 60%CO2/20%O2/20%N2 and 60%CO2/10%O2/30%N2 had the best effect to maintain the original odor profiles of salmon. The correlation analysis demonstrated that microbial growth had a strong relationship with myofibrillar and sarcoplasmic protein content. It can be concluded that 60%CO2/10%O2/30%N2 displayed the best effect to achieve the goal of preventing protein degradation and odor changes in salmon fillets.