Sodium hypochlorite solution has a good bacterial reduction effect. Thus, in order to understand the effect of sodium hypochlorite on tilapia storage, in this study, tilapia fillets were treated with sodium hypochlorite and Proclin 300 rinsing, the activity of histatinase protease was measured, and the muscle quality was assessed by the texture, colour, pH, myofibrillar fibril fragmentation index (MFI) and its structural changes. The results showed that sodium hypochlorite rinsing could significantly reduce the activities of histatinase enzymes B, L and D. Meanwhile, the sodium hypochlorite-treated group showed less degradation of myosin heavy chain, pro-myosin and myosin light chain, less degradation of texture and colour, better integrity in the fish myocytes, and a lower myofibrillar fragmentation index (MFI). In conclusion, sodium hypochlorite improved the storage quality of tilapia in several ways. Firstly, it inhibited protease activity, thereby maintaining the structural integrity of fish muscle fibres. Secondly, it reduced the rate of deterioration during storage.