This study investigated quality changes in oysters during frozen storage through physicochemical analysis, quantitative lipidomics, and quantitative proteomics. Results showed that the quality of oysters progressively deteriorated with increasing freezing time and temperature, as evidenced by color darkening, texture softening, reduced water-holding capacity, and increased TVB-N levels. Simultaneously, protein oxidation and lipid oxidation were observed, resulting in increased carbonyl, disulfide bonds, dityrosine, TBARS, and Schiff base content, and decreased free sulfhydryl groups. Lipidomics analysis revealed oxidation and hydrolysis of polyunsaturated lipids in oysters during storage, with PC being preferentially oxidized. Proteomics analysis revealed extensive oxidation and degradation of structural proteins, particularly MHC and filamin-C. Correlation analysis further highlighted oxidative degradation of polyunsaturated lipids and structural proteins as major contributors to the quality decline of oysters during frozen storage. This study sheds light on the mechanisms of quality deterioration in frozen oysters and provides valuable guidance for enhancing their preservation quality.