Dry/reimmersed storage is often used in the transportation of live scallops. In this study, tandem mass tag (TMT)labeled protein omics were used to quantitatively analyze the protein changes in scallops during dry/reimmersed stress. The results showed that during dry storage, scallops maintained cellular redox homeostasis through the upregulation of SCO1-like protein and thioredoxin domain-containing protein and reduced organic acids from the ATP synthetic process by the downregulation of NADH dehydrogenase, thereby reducing the damage caused during dry storage. During reimmersed storage, mitochondrial proteins underwent very sensitive changes. By upregulating aerobic respiration-related proteins (including proteins involved in glucose phosphate metabolism, glyceraldehyde 3-phosphate metabolism, etc.), the ATP synthesis ability was improved. However, the damage to the mitochondrial structure by dry storage could not be completely recovered, even by reimmersion. This included some apoptosis-related proteins that were obviously upregulated. In summary, compared with ATP-related indexes, mitochondria can respond more sensitively to dry storage stress.