This study investigates the effects of cathepsins on the gel strength and water-holding capacity (WHC) of myofibrillar protein gels from bighead carp (Aristichthys nobilis) under a hydroxyl radical-generation oxidizing system. The myofibrillar proteins were divided into control group (with cathepsins) and E64 group (without cathepsins). The changes of cathepsin B and cathepsin L activities, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), protein oxidation (total sulfhydryl and carbonyl contents), and chemical interactions (nonspecific association, ionic bonds, hydrogen bonds, hydrophobic interactions, and disulfides) of myofibrillar protein and gels, as well as the gel strength and WHC of two groups under 0–100 mM H2O2, were measured. The results indicated that mild oxidation (10 mM H2O2) made a better gel strength and WHC. Cathepsin B and L activities decreased with increasing H2O2 concentrations but their effects on myofibrillar protein degradation still existed during 0.1–50 mM H2O2, which was expressed by higher carbonyl contents and ionic bonds at 0.1 and 50 mM H2O2, higher total sulfhydryl contents at 0 mM H2O2, and a lower intensity of MHC and actin of the control group than the E64 group. Besides more protein degradation, cathepsin proteolysis also resulted in lower gel strength and WHC in control gels than E64 gels under mild oxidation, which could be explained by lower hydrophobic interaction and moderate disulfides bonds between gel protein molecules of control gels.