The Solenaia oleivora is an important freshwater economically farmed shellfish, and the traditional hooking method often causes different degrees of gill damage to the S. oleivora. Therefore, in this study, we investigated the mechanism of wound-healing in gill injuries in the freshwater mussel S. oleivora by simulating varying degrees of gill injury. It was found that the rates of oxygen consumption, ammonia excretion, and feeding did not change significantly in the mild-injury group at 2 and 12 h post-injury, while the rates were significantly lower in the severe-injury group compared with the control group, likely due to impairment of the respiratory metabolism. The rates of oxygen consumption, feeding, and ammonia excretion increased significantly in the mild-injury group at 24, 48, 72 h, compared with the control, as well as in the severe-injury group at 72 h post-injury, possibly due to increased energy requirements for tissue repair. Histological and transcriptomic analyses of tissues showed that in the mild-injury group at 2 and 12 h, blood cells migrated toward the wound, plugging it and triggering an inflammatory response associated with upregulation of TNF signaling, immune-related genes, and genes associated with the actin cytoskeleton, suggesting wound contraction and phagocytosis of blood cells. At 24 h post-injury, genes and pathways associated with antioxidant enzymes, chaperonins, autophagy, lysosomes, biochemical pathways, and energy metabolism were activated, suggesting a transition from an inflammatory response to an epithelialization process. At 48 h post-injury, Toll and Imd signaling were downregulated, together with upregulation of genes associated with the extracellular matrix, such as collagen, integrins, and glycoproteins, promoting epithelialization of the wound. After 72 h, proline and arginine metabolism were increased, as well as expression of mitochondrial genes. The severe-injury group showed reduced amino acid metabolism and activation of primary immunodeficiencies after 2 and 12 h, suggesting disturbances in metabolism and immunity, while after 2, 12, 24, and 48 h, genes related to the actin cytoskeleton, lipid metabolism, glycolysis, glycosyltransferases, chaperonins, guanylate-binding proteins, and NOD-like receptors were upregulated to promote wound contraction and inflammatory responses. At 72 h after injury, interleukin-4 and thymosin β-4 were activated and the NF-κB signaling pathway was inhibited to reduce inflammation, while epithelialization of the wounds was visible on tissue sections, possibly facilitated by the upregulation of ribosomal proteins, ATP. This study provides new insights into the mechanism of gill wound-healing in S oleivora.