Multi-omics techniques were combined with microstructure, molecular sensory science and non-volatile matrices for the first time to investigate variations in organic macromolecules and flavor in caviar during preservation. After 4–6 weeks of storage, the peroxide value was 35.38 mg/g and the accumulation of thiobarbiturates was significant with caviar membranes exhibiting a decrease in elasticity and an increase in viscosity. Sixteen key volatile compounds were detected by GC–MS, while the volatile compounds that contributed to the differences in caviar flavor at different storage times were mainly tetradecane, (E)-2-hexenal, and heptanal. The pathways associated with flavor release during storage were mainly abundant in the linolenic acid metabolism, alanine metabolism, and glycerophospholipid metabolism pathways. The correlation of 11 differential proteins and 24 differential lipids with odorants was further explored, such as arginine, proline, alanine, PE (20:4/22:6), PE (16:1/18:2), and PE (20:5/18:2). Overall, Aspartate, glutamate, oleic acid, linoleic acid, and phospholipids enriched in C22:6 and C18:2 chains are potential metabolic markers. This study provides a basis from a multi-omics perspective for the investigation of the relationship between quality deterioration and precursor metabolism in caviar storage process.