The quality of fish can change due to differences in the lipid and protein oxidation rates in different muscles. This study examined vacuum-packed eye muscle (EM), dorsal muscle (DM), belly muscle (BM), and tail muscle (TM) of bighead carp frozen for 180 days. The results reveal that EM had the highest lipid content and the lowest protein content, while DM had the lowest lipid content and the highest protein content. EM also showed the highest values of centrifugal loss and cooking loss, and the correlation analysis showed that these losses were positively correlated with dityrosine content and negatively correlated with conjugated triene content. The content of carbonyl, disulfide bond, and surface hydrophobicity of myofibrillar protein (MP) also increased with time, with DM having the highest values. The microstructure of EM was looser than other muscles. Therefore, DM had the fastest oxidation rate and EM had the lowest water holding capacity.